phenoml 0.0.17__tar.gz → 0.0.19__tar.gz

{phenoml-0.0.17 → phenoml-0.0.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phenoml
-Version: 0.0.17
+Version: 0.0.19
 Summary: 
 Requires-Python: >=3.8,<4.0
 Classifier: Intended Audience :: Developers

{phenoml-0.0.17 → phenoml-0.0.19}/pyproject.toml

@@ -3,7 +3,7 @@ name = "phenoml"
 
 [tool.poetry]
 name = "phenoml"
-version = "v0.0.17"
+version = "0.0.19"
 description = ""
 readme = "README.md"
 authors = []

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/agent/__init__.py

@@ -8,6 +8,7 @@ from .types import (
     AgentCreateRequestProvider,
     AgentDeleteResponse,
     AgentGetChatMessagesRequestOrder,
+    AgentGetChatMessagesRequestRole,
     AgentGetChatMessagesResponse,
     AgentListResponse,
     AgentPromptsResponse,
@@ -15,6 +16,7 @@ from .types import (
     AgentTemplate,
     AgentTemplateProvider,
     ChatMessageTemplate,
+    ChatMessageTemplateRole,
     ChatSessionTemplate,
     JsonPatch,
     JsonPatchOperation,
@@ -32,6 +34,7 @@ __all__ = [
     "AgentCreateRequestProvider",
     "AgentDeleteResponse",
     "AgentGetChatMessagesRequestOrder",
+    "AgentGetChatMessagesRequestRole",
     "AgentGetChatMessagesResponse",
     "AgentListResponse",
     "AgentPromptsResponse",
@@ -40,6 +43,7 @@ __all__ = [
     "AgentTemplateProvider",
     "BadRequestError",
     "ChatMessageTemplate",
+    "ChatMessageTemplateRole",
     "ChatSessionTemplate",
     "ForbiddenError",
     "InternalServerError",

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/agent/client.py

@@ -10,6 +10,7 @@ from .types.agent_chat_response import AgentChatResponse
 from .types.agent_create_request_provider import AgentCreateRequestProvider
 from .types.agent_delete_response import AgentDeleteResponse
 from .types.agent_get_chat_messages_request_order import AgentGetChatMessagesRequestOrder
+from .types.agent_get_chat_messages_request_role import AgentGetChatMessagesRequestRole
 from .types.agent_get_chat_messages_response import AgentGetChatMessagesResponse
 from .types.agent_list_response import AgentListResponse
 from .types.agent_response import AgentResponse
@@ -412,7 +413,7 @@ class AgentClient:
         *,
         chat_session_id: str,
         num_messages: typing.Optional[int] = None,
-        role: typing.Optional[str] = None,
+        role: typing.Optional[AgentGetChatMessagesRequestRole] = None,
         order: typing.Optional[AgentGetChatMessagesRequestOrder] = None,
         request_options: typing.Optional[RequestOptions] = None,
     ) -> AgentGetChatMessagesResponse:
@@ -427,8 +428,15 @@ class AgentClient:
         num_messages : typing.Optional[int]
             Number of messages to return
 
-        role : typing.Optional[str]
-            Filter by role
+        role : typing.Optional[AgentGetChatMessagesRequestRole]
+            Filter by one or more message roles. Multiple roles can be specified as a comma-separated string.
+            If not specified, messages with all roles are returned.
+
+            **Available roles:**
+            - `user` - Messages from the user
+            - `assistant` - Text responses from the AI assistant
+            - `model` - Function/tool call requests from the model
+            - `function` - Function/tool call results
 
         order : typing.Optional[AgentGetChatMessagesRequestOrder]
             Order of messages
@@ -451,7 +459,7 @@ class AgentClient:
         client.agent.get_chat_messages(
             chat_session_id="chat_session_id",
             num_messages=1,
-            role="role",
+            role="user",
             order="asc",
         )
         """
@@ -914,7 +922,7 @@ class AsyncAgentClient:
         *,
         chat_session_id: str,
         num_messages: typing.Optional[int] = None,
-        role: typing.Optional[str] = None,
+        role: typing.Optional[AgentGetChatMessagesRequestRole] = None,
         order: typing.Optional[AgentGetChatMessagesRequestOrder] = None,
         request_options: typing.Optional[RequestOptions] = None,
     ) -> AgentGetChatMessagesResponse:
@@ -929,8 +937,15 @@ class AsyncAgentClient:
         num_messages : typing.Optional[int]
             Number of messages to return
 
-        role : typing.Optional[str]
-            Filter by role
+        role : typing.Optional[AgentGetChatMessagesRequestRole]
+            Filter by one or more message roles. Multiple roles can be specified as a comma-separated string.
+            If not specified, messages with all roles are returned.
+
+            **Available roles:**
+            - `user` - Messages from the user
+            - `assistant` - Text responses from the AI assistant
+            - `model` - Function/tool call requests from the model
+            - `function` - Function/tool call results
 
         order : typing.Optional[AgentGetChatMessagesRequestOrder]
             Order of messages
@@ -958,7 +973,7 @@ class AsyncAgentClient:
             await client.agent.get_chat_messages(
                 chat_session_id="chat_session_id",
                 num_messages=1,
-                role="role",
+                role="user",
                 order="asc",
             )
 

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/agent/raw_client.py

@@ -19,6 +19,7 @@ from .types.agent_chat_response import AgentChatResponse
 from .types.agent_create_request_provider import AgentCreateRequestProvider
 from .types.agent_delete_response import AgentDeleteResponse
 from .types.agent_get_chat_messages_request_order import AgentGetChatMessagesRequestOrder
+from .types.agent_get_chat_messages_request_role import AgentGetChatMessagesRequestRole
 from .types.agent_get_chat_messages_response import AgentGetChatMessagesResponse
 from .types.agent_list_response import AgentListResponse
 from .types.agent_response import AgentResponse
@@ -770,7 +771,7 @@ class RawAgentClient:
         *,
         chat_session_id: str,
         num_messages: typing.Optional[int] = None,
-        role: typing.Optional[str] = None,
+        role: typing.Optional[AgentGetChatMessagesRequestRole] = None,
         order: typing.Optional[AgentGetChatMessagesRequestOrder] = None,
         request_options: typing.Optional[RequestOptions] = None,
     ) -> HttpResponse[AgentGetChatMessagesResponse]:
@@ -785,8 +786,15 @@ class RawAgentClient:
         num_messages : typing.Optional[int]
             Number of messages to return
 
-        role : typing.Optional[str]
-            Filter by role
+        role : typing.Optional[AgentGetChatMessagesRequestRole]
+            Filter by one or more message roles. Multiple roles can be specified as a comma-separated string.
+            If not specified, messages with all roles are returned.
+
+            **Available roles:**
+            - `user` - Messages from the user
+            - `assistant` - Text responses from the AI assistant
+            - `model` - Function/tool call requests from the model
+            - `function` - Function/tool call results
 
         order : typing.Optional[AgentGetChatMessagesRequestOrder]
             Order of messages
@@ -1603,7 +1611,7 @@ class AsyncRawAgentClient:
         *,
         chat_session_id: str,
         num_messages: typing.Optional[int] = None,
-        role: typing.Optional[str] = None,
+        role: typing.Optional[AgentGetChatMessagesRequestRole] = None,
         order: typing.Optional[AgentGetChatMessagesRequestOrder] = None,
         request_options: typing.Optional[RequestOptions] = None,
     ) -> AsyncHttpResponse[AgentGetChatMessagesResponse]:
@@ -1618,8 +1626,15 @@ class AsyncRawAgentClient:
         num_messages : typing.Optional[int]
             Number of messages to return
 
-        role : typing.Optional[str]
-            Filter by role
+        role : typing.Optional[AgentGetChatMessagesRequestRole]
+            Filter by one or more message roles. Multiple roles can be specified as a comma-separated string.
+            If not specified, messages with all roles are returned.
+
+            **Available roles:**
+            - `user` - Messages from the user
+            - `assistant` - Text responses from the AI assistant
+            - `model` - Function/tool call requests from the model
+            - `function` - Function/tool call results
 
         order : typing.Optional[AgentGetChatMessagesRequestOrder]
             Order of messages

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/agent/types/__init__.py

@@ -7,6 +7,7 @@ from .agent_create_request import AgentCreateRequest
 from .agent_create_request_provider import AgentCreateRequestProvider
 from .agent_delete_response import AgentDeleteResponse
 from .agent_get_chat_messages_request_order import AgentGetChatMessagesRequestOrder
+from .agent_get_chat_messages_request_role import AgentGetChatMessagesRequestRole
 from .agent_get_chat_messages_response import AgentGetChatMessagesResponse
 from .agent_list_response import AgentListResponse
 from .agent_prompts_response import AgentPromptsResponse
@@ -14,6 +15,7 @@ from .agent_response import AgentResponse
 from .agent_template import AgentTemplate
 from .agent_template_provider import AgentTemplateProvider
 from .chat_message_template import ChatMessageTemplate
+from .chat_message_template_role import ChatMessageTemplateRole
 from .chat_session_template import ChatSessionTemplate
 from .json_patch import JsonPatch
 from .json_patch_operation import JsonPatchOperation
@@ -27,6 +29,7 @@ __all__ = [
     "AgentCreateRequestProvider",
     "AgentDeleteResponse",
     "AgentGetChatMessagesRequestOrder",
+    "AgentGetChatMessagesRequestRole",
     "AgentGetChatMessagesResponse",
     "AgentListResponse",
     "AgentPromptsResponse",
@@ -34,6 +37,7 @@ __all__ = [
     "AgentTemplate",
     "AgentTemplateProvider",
     "ChatMessageTemplate",
+    "ChatMessageTemplateRole",
     "ChatSessionTemplate",
     "JsonPatch",
     "JsonPatchOperation",

phenoml-0.0.19/src/phenoml/agent/types/agent_get_chat_messages_request_role.py

@@ -0,0 +1,5 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+AgentGetChatMessagesRequestRole = typing.Union[typing.Literal["user", "assistant", "model", "function"], typing.Any]

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/agent/types/chat_message_template.py

@@ -4,6 +4,7 @@ import typing
 
 import pydantic
 from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from .chat_message_template_role import ChatMessageTemplateRole
 
 
 class ChatMessageTemplate(UniversalBaseModel):
@@ -17,9 +18,13 @@ class ChatMessageTemplate(UniversalBaseModel):
     Chat session ID
     """
 
-    role: typing.Optional[str] = pydantic.Field(default=None)
+    role: typing.Optional[ChatMessageTemplateRole] = pydantic.Field(default=None)
     """
-    Message role
+    Message role indicating the source/type of the message:
+    - `user` - Messages from the user
+    - `assistant` - Text responses from the AI assistant
+    - `model` - Function/tool call requests to the model
+    - `function` - Function/tool call results
     """
 
     content: typing.Optional[str] = pydantic.Field(default=None)

phenoml-0.0.19/src/phenoml/agent/types/chat_message_template_role.py

@@ -0,0 +1,5 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+ChatMessageTemplateRole = typing.Union[typing.Literal["user", "assistant", "model", "function"], typing.Any]

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/construe/types/extract_request_config.py

@@ -16,7 +16,10 @@ class ExtractRequestConfig(UniversalBaseModel):
 
     max_codes_per_chunk: typing.Optional[int] = pydantic.Field(default=None)
     """
-    Maximum number of codes to extract per chunk
+    Maximum number of codes to extract per chunk. If not specified, uses system-specific defaults:
+    * SNOMED: 10
+    * LOINC, HPO, RXNORM: 20
+    * All other systems: 5
     """
 
     code_similarity_filter: typing.Optional[float] = pydantic.Field(default=None)
@@ -42,6 +45,11 @@ class ExtractRequestConfig(UniversalBaseModel):
     Whether to include ancestor/parent codes in the results
     """
 
+    include_invalid: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether to include codes that failed validation in the results
+    """
+
     if IS_PYDANTIC_V2:
         model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
     else:

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/construe/types/extracted_code_result.py

@@ -19,6 +19,11 @@ class ExtractedCodeResult(UniversalBaseModel):
     Short description of the code
     """
 
+    valid: bool = pydantic.Field()
+    """
+    Whether the code passed validation. Always true unless include_invalid is set to true, in which case invalid codes will have this set to false.
+    """
+
     long_description: typing_extensions.Annotated[typing.Optional[str], FieldMetadata(alias="longDescription")] = (
         pydantic.Field(default=None)
     )

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/core/client_wrapper.py

@@ -22,10 +22,10 @@ class BaseClientWrapper:
 
     def get_headers(self) -> typing.Dict[str, str]:
         headers: typing.Dict[str, str] = {
-            "User-Agent": "phenoml/v0.0.17",
+            "User-Agent": "phenoml/0.0.19",
             "X-Fern-Language": "Python",
             "X-Fern-SDK-Name": "phenoml",
-            "X-Fern-SDK-Version": "v0.0.17",
+            "X-Fern-SDK-Version": "0.0.19",
             **(self.get_custom_headers() or {}),
         }
         headers["Authorization"] = f"Bearer {self._get_token()}"

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/fhir_provider/__init__.py

@@ -7,9 +7,11 @@ from .types import (
     FhirProviderAuthConfig,
     FhirProviderDeleteResponse,
     FhirProviderListResponse,
+    FhirProviderListResponseFhirProvidersItem,
     FhirProviderRemoveAuthConfigResponse,
     FhirProviderResponse,
-    FhirProviderSetActiveAuthConfigResponse,
+    FhirProviderResponseData,
+    FhirProviderSandboxInfo,
     FhirProviderTemplate,
     FhirQueryResponse,
     FhirQueryResponseData,
@@ -17,6 +19,7 @@ from .types import (
     Provider,
     Role,
     ServiceAccountKey,
+    ServiceAccountMetadata,
     SmartConfiguration,
 )
 from .errors import BadRequestError, ForbiddenError, InternalServerError, NotFoundError, UnauthorizedError
@@ -27,9 +30,11 @@ __all__ = [
     "FhirProviderAuthConfig",
     "FhirProviderDeleteResponse",
     "FhirProviderListResponse",
+    "FhirProviderListResponseFhirProvidersItem",
     "FhirProviderRemoveAuthConfigResponse",
     "FhirProviderResponse",
-    "FhirProviderSetActiveAuthConfigResponse",
+    "FhirProviderResponseData",
+    "FhirProviderSandboxInfo",
     "FhirProviderTemplate",
     "FhirQueryResponse",
     "FhirQueryResponseData",
@@ -40,6 +45,7 @@ __all__ = [
     "Provider",
     "Role",
     "ServiceAccountKey",
+    "ServiceAccountMetadata",
     "SmartConfiguration",
     "UnauthorizedError",
 ]

{phenoml-0.0.17 → phenoml-0.0.19}/src/phenoml/fhir_provider/client.py

@@ -11,7 +11,6 @@ from .types.fhir_provider_delete_response import FhirProviderDeleteResponse
 from .types.fhir_provider_list_response import FhirProviderListResponse
 from .types.fhir_provider_remove_auth_config_response import FhirProviderRemoveAuthConfigResponse
 from .types.fhir_provider_response import FhirProviderResponse
-from .types.fhir_provider_set_active_auth_config_response import FhirProviderSetActiveAuthConfigResponse
 from .types.provider import Provider
 from .types.role import Role
 from .types.service_account_key import ServiceAccountKey
@@ -51,7 +50,9 @@ class FhirProviderClient:
         request_options: typing.Optional[RequestOptions] = None,
     ) -> FhirProviderResponse:
         """
-        Creates a new FHIR provider configuration with authentication credentials
+        Creates a new FHIR provider configuration with authentication credentials.
+
+        Note: The "sandbox" provider type cannot be created via this API - it is managed internally.
 
         Parameters
         ----------
@@ -120,7 +121,10 @@ class FhirProviderClient:
 
     def list(self, *, request_options: typing.Optional[RequestOptions] = None) -> FhirProviderListResponse:
         """
-        Retrieves a list of all active FHIR providers for the authenticated user
+        Retrieves a list of all active FHIR providers for the authenticated user.
+
+        On shared instances, only sandbox providers are returned.
+        Sandbox providers return FhirProviderSandboxInfo.
 
         Parameters
         ----------
@@ -148,7 +152,10 @@ class FhirProviderClient:
         self, fhir_provider_id: str, *, request_options: typing.Optional[RequestOptions] = None
     ) -> FhirProviderResponse:
         """
-        Retrieves a specific FHIR provider configuration by its ID
+        Retrieves a specific FHIR provider configuration by its ID.
+
+        Sandbox providers return FhirProviderSandboxInfo.
+        On shared instances, only sandbox providers can be accessed.
 
         Parameters
         ----------
@@ -181,7 +188,9 @@ class FhirProviderClient:
         self, fhir_provider_id: str, *, request_options: typing.Optional[RequestOptions] = None
     ) -> FhirProviderDeleteResponse:
         """
-        Soft deletes a FHIR provider by setting is_active to false
+        Soft deletes a FHIR provider by setting is_active to false.
+
+        Note: Sandbox providers cannot be deleted.
 
         Parameters
         ----------
@@ -223,7 +232,10 @@ class FhirProviderClient:
         request_options: typing.Optional[RequestOptions] = None,
     ) -> FhirProviderResponse:
         """
-        Adds a new authentication configuration to an existing FHIR provider. This enables key rotation and multiple auth configurations per provider.
+        Adds a new authentication configuration to an existing FHIR provider.
+        This enables key rotation and multiple auth configurations per provider.
+
+        Note: Sandbox providers cannot be modified.
 
         Parameters
         ----------
@@ -279,9 +291,15 @@ class FhirProviderClient:
 
     def set_active_auth_config(
         self, fhir_provider_id: str, *, auth_config_id: str, request_options: typing.Optional[RequestOptions] = None
-    ) -> FhirProviderSetActiveAuthConfigResponse:
+    ) -> FhirProviderResponse:
         """
-        Sets which authentication configuration should be active for a FHIR provider. Only one auth config can be active at a time.
+        Sets which authentication configuration should be active for a FHIR provider.
+        Only one auth config can be active at a time.
+
+        If the specified auth config is already active, the request succeeds without
+        making any changes and returns a message indicating the config is already active.
+
+        Note: Sandbox providers cannot be modified.
 
         Parameters
         ----------
@@ -296,8 +314,9 @@ class FhirProviderClient:
 
         Returns
         -------
-        FhirProviderSetActiveAuthConfigResponse
-            Active auth configuration set successfully
+        FhirProviderResponse
+            Active auth configuration set successfully, or the config was already active.
+            Check the message field to determine which case occurred.
 
         Examples
         --------
@@ -320,7 +339,10 @@ class FhirProviderClient:
         self, fhir_provider_id: str, *, auth_config_id: str, request_options: typing.Optional[RequestOptions] = None
     ) -> FhirProviderRemoveAuthConfigResponse:
         """
-        Removes an authentication configuration from a FHIR provider. Cannot remove the currently active auth configuration.
+        Removes an authentication configuration from a FHIR provider.
+        Cannot remove the currently active auth configuration.
+
+        Note: Sandbox providers cannot be modified.
 
         Parameters
         ----------
@@ -387,7 +409,9 @@ class AsyncFhirProviderClient:
         request_options: typing.Optional[RequestOptions] = None,
     ) -> FhirProviderResponse:
         """
-        Creates a new FHIR provider configuration with authentication credentials
+        Creates a new FHIR provider configuration with authentication credentials.
+
+        Note: The "sandbox" provider type cannot be created via this API - it is managed internally.
 
         Parameters
         ----------
@@ -464,7 +488,10 @@ class AsyncFhirProviderClient:
 
     async def list(self, *, request_options: typing.Optional[RequestOptions] = None) -> FhirProviderListResponse:
         """
-        Retrieves a list of all active FHIR providers for the authenticated user
+        Retrieves a list of all active FHIR providers for the authenticated user.
+
+        On shared instances, only sandbox providers are returned.
+        Sandbox providers return FhirProviderSandboxInfo.
 
         Parameters
         ----------
@@ -500,7 +527,10 @@ class AsyncFhirProviderClient:
         self, fhir_provider_id: str, *, request_options: typing.Optional[RequestOptions] = None
     ) -> FhirProviderResponse:
         """
-        Retrieves a specific FHIR provider configuration by its ID
+        Retrieves a specific FHIR provider configuration by its ID.
+
+        Sandbox providers return FhirProviderSandboxInfo.
+        On shared instances, only sandbox providers can be accessed.
 
         Parameters
         ----------
@@ -541,7 +571,9 @@ class AsyncFhirProviderClient:
         self, fhir_provider_id: str, *, request_options: typing.Optional[RequestOptions] = None
     ) -> FhirProviderDeleteResponse:
         """
-        Soft deletes a FHIR provider by setting is_active to false
+        Soft deletes a FHIR provider by setting is_active to false.
+
+        Note: Sandbox providers cannot be deleted.
 
         Parameters
         ----------
@@ -591,7 +623,10 @@ class AsyncFhirProviderClient:
         request_options: typing.Optional[RequestOptions] = None,
     ) -> FhirProviderResponse:
         """
-        Adds a new authentication configuration to an existing FHIR provider. This enables key rotation and multiple auth configurations per provider.
+        Adds a new authentication configuration to an existing FHIR provider.
+        This enables key rotation and multiple auth configurations per provider.
+
+        Note: Sandbox providers cannot be modified.
 
         Parameters
         ----------
@@ -655,9 +690,15 @@ class AsyncFhirProviderClient:
 
     async def set_active_auth_config(
         self, fhir_provider_id: str, *, auth_config_id: str, request_options: typing.Optional[RequestOptions] = None
-    ) -> FhirProviderSetActiveAuthConfigResponse:
+    ) -> FhirProviderResponse:
         """
-        Sets which authentication configuration should be active for a FHIR provider. Only one auth config can be active at a time.
+        Sets which authentication configuration should be active for a FHIR provider.
+        Only one auth config can be active at a time.
+
+        If the specified auth config is already active, the request succeeds without
+        making any changes and returns a message indicating the config is already active.
+
+        Note: Sandbox providers cannot be modified.
 
         Parameters
         ----------
@@ -672,8 +713,9 @@ class AsyncFhirProviderClient:
 
         Returns
         -------
-        FhirProviderSetActiveAuthConfigResponse
-            Active auth configuration set successfully
+        FhirProviderResponse
+            Active auth configuration set successfully, or the config was already active.
+            Check the message field to determine which case occurred.
 
         Examples
         --------
@@ -704,7 +746,10 @@ class AsyncFhirProviderClient:
         self, fhir_provider_id: str, *, auth_config_id: str, request_options: typing.Optional[RequestOptions] = None
     ) -> FhirProviderRemoveAuthConfigResponse:
         """
-        Removes an authentication configuration from a FHIR provider. Cannot remove the currently active auth configuration.
+        Removes an authentication configuration from a FHIR provider.
+        Cannot remove the currently active auth configuration.
+
+        Note: Sandbox providers cannot be modified.
 
         Parameters
         ----------