sapiopycommons 2025.9.5a726__py3-none-any.whl → 2025.9.8a728__py3-none-any.whl

sapiopycommons/ai/tool_service_base.py

@@ -29,6 +29,7 @@ from sapiopycommons.ai.protoapi.session.sapio_conn_info_pb2 import SapioUserSecr
 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
 
 
@@ -318,8 +319,8 @@ class ToolServiceBase(ToolServiceServicer, ABC):
             # 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 tools "
-                        f"for this service are: \n{all_tool_names}")
+            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.
@@ -329,7 +330,8 @@ class ToolServiceBase(ToolServiceServicer, ABC):
             tool.setup(user, request, context)
             # 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)} instead."
+                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.
@@ -347,6 +349,9 @@ class ToolServiceBase(ToolServiceServicer, ABC):
         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.
+            tool.temp_data.cleanup()
 
 
 class ToolBase(ABC):
@@ -366,6 +371,8 @@ class ToolBase(ABC):
     logger: Logger
     verbose_logging: bool
 
+    temp_data: TempFileHandler
+
     user: SapioUser
     request: ProcessStepRequestPbo
     context: ServicerContext
@@ -403,6 +410,7 @@ class ToolBase(ABC):
         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)
@@ -528,8 +536,8 @@ class ToolBase(ABC):
         """
         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,
-                                 optional: bool = False) -> None:
+    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.
@@ -552,9 +560,9 @@ class ToolBase(ABC):
             )
         ))
 
-    def add_double_config_field(self, field_name: str, display_name: str, description: str, default_value: float,
-                                min_value: float = -10.**120, max_value: float = 10.**120, precision: int = 2,
-                                optional: bool = False) -> None:
+    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.
@@ -584,7 +592,7 @@ class ToolBase(ABC):
         ))
 
     def add_integer_config_field(self, field_name: str, display_name: str, description: str,
-                                 default_value: int, min_value: int = -2**31, max_value: int = 2**31-1,
+                                 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
@@ -613,7 +621,8 @@ class ToolBase(ABC):
         ))
 
     def add_string_config_field(self, field_name: str, display_name: str, description: str,
-                                default_value: str, max_length: int = 1000, optional: bool = False) -> None:
+                                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.
@@ -638,8 +647,9 @@ class ToolBase(ABC):
             )
         ))
 
-    def add_list_config_field(self, field_name: str, display_name: str, description: str, default_value: str,
-                              allowed_values: list[str], direct_edit: bool = False, optional: bool = False) -> 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) -> None:
         """
         Add a list configuration field to the tool. This field will be used to configure the tool in the plan
         manager.
@@ -668,8 +678,8 @@ class ToolBase(ABC):
         ))
 
     def add_multi_list_config_field(self, field_name: str, display_name: str, description: str,
-                                    default_value: list[str], allowed_values: list[str], direct_edit: bool = False,
-                                    optional: bool = False) -> None:
+                                    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.
@@ -691,7 +701,7 @@ class ToolBase(ABC):
             required=not optional,
             editable=True,
             selection_properties=SelectionPropertiesPbo(
-                default_value=",".join(default_value),
+                default_value=",".join(default_value) if default_value else None,
                 static_list_values=allowed_values,
                 multi_select=True,
                 direct_edit=direct_edit,

sapiopycommons/files/temp_files.py

@@ -0,0 +1,49 @@
+import os
+import shutil
+import tempfile
+
+
+# FR-47422: Created class.
+class TempFileHandler:
+    """
+    A utility class to manage temporary files and directories.
+    """
+    directories: list[str]
+    files: list[str]
+
+    def __init__(self) -> None:
+        self.directories = []
+        self.files = []
+
+    def create_temp_directory(self) -> str:
+        """
+        :return: The path to a newly created temporary directory.
+        """
+        directory: str = tempfile.mkdtemp()
+        self.directories.append(directory)
+        return directory
+
+    def create_temp_file(self, data: str | bytes, suffix: str = "") -> str:
+        """
+        :param data: The data to write to the temporary file.
+        :param suffix: An optional suffix for the temporary file.
+        :return: The path to a newly created temporary file containing the provided data.
+        """
+        mode: str = 'w' if isinstance(data, str) else 'wb'
+        with tempfile.NamedTemporaryFile(mode=mode, suffix=suffix, delete=False) as tmp_file:
+            tmp_file.write(data)
+            file_path: str = tmp_file.name
+            self.files.append(file_path)
+        return file_path
+
+    def cleanup(self) -> None:
+        """
+        Delete all temporary files and directories created by this handler.
+        """
+        for directory in self.directories:
+            if os.path.exists(directory):
+                shutil.rmtree(directory)
+
+        for file_path in self.files:
+            if os.path.exists(file_path):
+                os.remove(file_path)

{sapiopycommons-2025.9.5a726.dist-info → sapiopycommons-2025.9.8a728.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.9.5a726
+Version: 2025.9.8a728
 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-2025.9.5a726.dist-info → sapiopycommons-2025.9.8a728.dist-info}/RECORD

@@ -4,7 +4,7 @@ sapiopycommons/ai/converter_service_base.py,sha256=TMSyEekbbqMk9dRuAtLlSJ1sA1H8K
 sapiopycommons/ai/protobuf_utils.py,sha256=cBjbxoFAwU02kNUxEce95WnMU2CMuDD-qFaeWgvQJMQ,24599
 sapiopycommons/ai/server.py,sha256=jvmAcs4y8qp0d483wCAUgPlSBSoUUQvCjv_OvQXEGUs,4274
 sapiopycommons/ai/test_client.py,sha256=iPhn7cvKNLmDAXrjpmIkZpW2pDWlUhJZHDLHJbEoWsg,15673
-sapiopycommons/ai/tool_service_base.py,sha256=Cj4ewRfBSiW1Tdzn4hkm9P-gDa6NS6fh4jc4TUmvNMs,45336
+sapiopycommons/ai/tool_service_base.py,sha256=AVW6Yf0l_l4x__dosIZyAJun4UmZAZaBJRYzNru_fD4,45806
 sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.py,sha256=8tKXwLXcqFGdQHHSEBSi6Fd7dcaCFoOqmhjzqhenb_M,2372
 sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.pyi,sha256=FwtXmNAf7iYGEFm4kbqb04v77jNHbZg18ZmEDhle_bU,1444
 sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2_grpc.py,sha256=uO25bcnfGqXpP4ggUur54Nr73Wj-DGWftExzLNcxdHI,931
@@ -66,6 +66,7 @@ sapiopycommons/files/file_data_handler.py,sha256=f96MlkMuQhUCi4oLnzJK5AiuElCp5jL
 sapiopycommons/files/file_util.py,sha256=djouyGjsYgWzjz2OBRnSeMDgj6NrsJUm1a2J93J8Wco,31915
 sapiopycommons/files/file_validator.py,sha256=ryg22-93csmRO_Pv0ZpWphNkB74xWZnHyJ23K56qLj0,28761
 sapiopycommons/files/file_writer.py,sha256=hACVl0duCjP28gJ1NPljkjagNCLod0ygUlPbvUmRDNM,17605
+sapiopycommons/files/temp_files.py,sha256=Puv59qtGwiXVJnTm4YuyeZPKw_leXDW906Uz_xbIt6A,1542
 sapiopycommons/flowcyto/flow_cyto.py,sha256=vs9WhXXKz3urpjL8QKSk56B-NSmQR3O3x_WFBKoeO10,3227
 sapiopycommons/flowcyto/flowcyto_data.py,sha256=mYKFuLbtpJ-EsQxLGtu4tNHVlygTxKixgJxJqD68F58,2596
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -98,7 +99,7 @@ sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 sapiopycommons/webhook/webhook_context.py,sha256=D793uLsb1691SalaPnBUk3rOSxn_hYLhdvkaIxjNXss,1909
 sapiopycommons/webhook/webhook_handlers.py,sha256=7o_wXOruhT9auNh8OfhJAh4WhhiPKij67FMBSpGPICc,39939
 sapiopycommons/webhook/webservice_handlers.py,sha256=cvW6Mk_110BzYqkbk63Kg7jWrltBCDALOlkJRu8h4VQ,14300
-sapiopycommons-2025.9.5a726.dist-info/METADATA,sha256=VLxZnp7_F2kc3BrihRHSG3dN_oeBhoDWNazF-dUWsDo,3142
-sapiopycommons-2025.9.5a726.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-sapiopycommons-2025.9.5a726.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2025.9.5a726.dist-info/RECORD,,
+sapiopycommons-2025.9.8a728.dist-info/METADATA,sha256=6IMqQ6KDSTEcXMpbfbwpBSC_eGnhn-336JCdZkvNmR0,3142
+sapiopycommons-2025.9.8a728.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+sapiopycommons-2025.9.8a728.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2025.9.8a728.dist-info/RECORD,,