sapiopycommons 2025.10.20a789__tar.gz → 2025.10.21a792__tar.gz

{sapiopycommons-2025.10.20a789 → sapiopycommons-2025.10.21a792}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.10.20a789
+Version: 2025.10.21a792
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>

{sapiopycommons-2025.10.20a789 → sapiopycommons-2025.10.21a792}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2025.10.20a789'
+version='2025.10.21a792'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2025.10.20a789 → sapiopycommons-2025.10.21a792}/src/sapiopycommons/ai/agent_service_base.py

@@ -336,9 +336,9 @@ class AgentServiceBase(ToolServiceServicer, ABC):
 
         # Instantiate the agent class.
         agent: AgentBase = registered_agents[find_agent]()
+        # Setup the agent with details from the request.
+        agent.setup(user, request, context, self.debug_mode)
         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):
@@ -387,14 +387,52 @@ class AgentBase(ABC):
 
     logs: list[str]
     logger: Logger
-    verbose_logging: bool
-
-    temp_data: TempFileHandler
-
-    user: SapioUser
-    request: ProcessStepRequestPbo
-    context: ServicerContext
-    debug_mode: bool
+    _verbose_logging: bool | None = None
+
+    _temp_data: TempFileHandler | None = None
+
+    _user: SapioUser | None = None
+    _request: ProcessStepRequestPbo | None = None
+    _context: ServicerContext | None = None
+    _debug_mode: bool | None = None
+    
+    __is_setup: bool
+
+    @property
+    def verbose_logging(self) -> bool:
+        if not self.__is_setup:
+            raise Exception("Agent must be set up to respond to a request before accessing this property.")
+        return self._verbose_logging
+
+    @property
+    def temp_data(self) -> TempFileHandler:
+        if not self.__is_setup:
+            raise Exception("Agent must be set up to respond to a request before accessing this property.")
+        return self._temp_data
+
+    @property
+    def user(self) -> SapioUser:
+        if not self.__is_setup:
+            raise Exception("Agent must be set up to respond to a request before accessing this property.")
+        return self._user
+
+    @property
+    def request(self) -> ProcessStepRequestPbo:
+        if not self.__is_setup:
+            raise Exception("Agent must be set up to respond to a request before accessing this property.")
+        return self._request
+
+    @property
+    def context(self) -> ServicerContext:
+        if not self.__is_setup:
+            raise Exception("Agent must be set up to respond to a request before accessing this property.")
+        return self._context
+
+    @property
+    def debug_mode(self) -> bool:
+        if not self.__is_setup:
+            raise Exception("Agent must be set up to respond to a request before accessing this property.")
+        return self._debug_mode
 
     @classmethod
     @abstractmethod
@@ -455,12 +493,12 @@ class AgentBase(ABC):
         return None
 
     def __init__(self):
+        self.__is_setup = False
         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)
@@ -477,11 +515,13 @@ class AgentBase(ABC):
         :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
+        self.__is_setup = True
+        self._user = user
+        self._request = request
+        self._context = context
+        self._verbose_logging = request.verbose_logging
+        self._debug_mode = debug_mode
+        self._temp_data = TempFileHandler()
 
     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,
@@ -939,35 +979,32 @@ class AgentBase(ABC):
         """
         pass
 
-    def get_credentials(self, category: str = None, host: str = None) -> ExternalCredentials:
+    def get_credentials(self, name: str | None = None, category: str | None = None) -> ExternalCredentials:
         """
         Get credentials for the given category and host.
 
+        :param name: The host name of the credentials to retrieve.
         :param category: The category of the credentials to retrieve.
-        :param host: The host for which to retrieve the credentials.
         :return: An ExternalCredentials object containing the credentials for the given category and host.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         # Remove leading/trailing whitespace
+        name = name.strip() if name else None
         category = category.strip() if category else None
-        host = host.strip() if host else None
 
         matching_creds: list[ExternalCredentialsPbo] = []
         for cred in self.request.external_credential:
             # Do case insensitive comparison
+            if name and cred.display_name.lower != name.lower():
+                continue
             if category and cred.category.lower() != category.lower():
                 continue
-            if host:
-                # Parse the URL to get the host and compare
-                from urllib.parse import urlparse
-                parsed_url = urlparse(cred.url)
-                if parsed_url.hostname is None or parsed_url.hostname.lower() != host.lower():
-                    continue
-
             matching_creds.append(cred)
         if len(matching_creds) == 0:
-            raise ValueError(f"No credentials found for category '{category}' and host '{host}'.")
+            raise ValueError(f"No credentials found for name '{name}' and category '{category}'.")
         if len(matching_creds) > 1:
-            raise ValueError(f"Multiple credentials found for category '{category}' and host '{host}'.")
+            raise ValueError(f"Multiple credentials found for name '{name}' and category '{category}'.")
 
         return ExternalCredentials.from_pbo(matching_creds[0])
 
@@ -978,6 +1015,8 @@ class AgentBase(ABC):
         :param value: The value of the credentials config field.
         :return: An ExternalCredentials object containing the credentials.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         # Values should be of the format "Name (Identifier)"
         match = re.match(r"^(.*) \((.*)\)$", value)
         if not match:
@@ -1004,23 +1043,34 @@ class AgentBase(ABC):
         """
         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)
+            p: CompletedProcess[str] = subprocess.run(args, check=True, capture_output=True, text=True, cwd=cwd,
+                                                      **kwargs)
+            if p.stdout:
+                self.log_info(f"STDOUT: {p.stdout}")
+            if p.stderr:
+                self.log_info(f"STDERR: {p.stderr}")
+            return p
         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}")
+            if e.stdout:
+                self.log_error(f"STDOUT: {e.stdout}")
+            if e.stderr:
+                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.
+        
+        Logging info can be done during initialization, but those logs will not be returned to the caller. Other
+        log calls will be returned to the caller, even if done during initialization.
 
         :param message: The message to log.
         """
         if not message:
             return
-        if self.verbose_logging:
+        if self.__is_setup and self.verbose_logging:
             self.logs.append(f"INFO: {self.name()}: {message}")
         self.logger.info(message)
 
@@ -1068,6 +1118,8 @@ class AgentBase(ABC):
         :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.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         return self.request.input[index].is_partial
 
     def get_input_name(self, index: int = 0) -> str | None:
@@ -1077,6 +1129,8 @@ class AgentBase(ABC):
         :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.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         return self.request.input[index].item_container.container_name
 
     def get_input_content_type(self, index: int = 0) -> ContentTypePbo:
@@ -1086,6 +1140,8 @@ class AgentBase(ABC):
         :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.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         return self.request.input[index].item_container.content_type
 
     def get_input_binary(self, index: int = 0) -> list[bytes]:
@@ -1095,6 +1151,8 @@ class AgentBase(ABC):
         :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.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         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.")
@@ -1109,6 +1167,8 @@ class AgentBase(ABC):
             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.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         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.")
@@ -1128,6 +1188,8 @@ class AgentBase(ABC):
         :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.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         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.")
@@ -1148,6 +1210,8 @@ class AgentBase(ABC):
         :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.
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         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.")
@@ -1175,6 +1239,8 @@ class AgentBase(ABC):
             (bool for boolean fields, float for double fields, int for short, integer, long, and enum fields, and
             string for everything else).
         """
+        if not self.__is_setup:
+            raise Exception("Cannot call this function before the agent has been set up to respond to a request.")
         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():