phenoml 0.0.8__py3-none-any.whl → 0.0.9__py3-none-any.whl

phenoml/agent/client.py

@@ -343,6 +343,8 @@ class AgentClient:
         *,
         message: str,
         agent_id: str,
+        phenoml_on_behalf_of: typing.Optional[str] = None,
+        phenoml_fhir_provider: typing.Optional[str] = None,
         context: typing.Optional[str] = OMIT,
         session_id: typing.Optional[str] = OMIT,
         request_options: typing.Optional[RequestOptions] = None,
@@ -358,6 +360,14 @@ class AgentClient:
         agent_id : str
             The ID of the agent to chat with
 
+        phenoml_on_behalf_of : typing.Optional[str]
+            Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
+            Must be in the format: Patient/{uuid} or Practitioner/{uuid}
+
+        phenoml_fhir_provider : typing.Optional[str]
+            Optional header for FHIR provider authentication. Contains credentials in the format {fhir_provider_id}:{oauth2_token}.
+            Multiple FHIR provider integrations can be provided as comma-separated values.
+
         context : typing.Optional[str]
             Optional context for the conversation
 
@@ -380,12 +390,20 @@ class AgentClient:
             token="YOUR_TOKEN",
         )
         client.agent.chat(
+            phenoml_on_behalf_of="Patient/550e8400-e29b-41d4-a716-446655440000",
+            phenoml_fhir_provider="550e8400-e29b-41d4-a716-446655440000:eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c...",
             message="What is the patient's current condition?",
             agent_id="agent-123",
         )
         """
         _response = self._raw_client.chat(
-            message=message, agent_id=agent_id, context=context, session_id=session_id, request_options=request_options
+            message=message,
+            agent_id=agent_id,
+            phenoml_on_behalf_of=phenoml_on_behalf_of,
+            phenoml_fhir_provider=phenoml_fhir_provider,
+            context=context,
+            session_id=session_id,
+            request_options=request_options,
         )
         return _response.data
 
@@ -819,6 +837,8 @@ class AsyncAgentClient:
         *,
         message: str,
         agent_id: str,
+        phenoml_on_behalf_of: typing.Optional[str] = None,
+        phenoml_fhir_provider: typing.Optional[str] = None,
         context: typing.Optional[str] = OMIT,
         session_id: typing.Optional[str] = OMIT,
         request_options: typing.Optional[RequestOptions] = None,
@@ -834,6 +854,14 @@ class AsyncAgentClient:
         agent_id : str
             The ID of the agent to chat with
 
+        phenoml_on_behalf_of : typing.Optional[str]
+            Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
+            Must be in the format: Patient/{uuid} or Practitioner/{uuid}
+
+        phenoml_fhir_provider : typing.Optional[str]
+            Optional header for FHIR provider authentication. Contains credentials in the format {fhir_provider_id}:{oauth2_token}.
+            Multiple FHIR provider integrations can be provided as comma-separated values.
+
         context : typing.Optional[str]
             Optional context for the conversation
 
@@ -861,6 +889,8 @@ class AsyncAgentClient:
 
         async def main() -> None:
             await client.agent.chat(
+                phenoml_on_behalf_of="Patient/550e8400-e29b-41d4-a716-446655440000",
+                phenoml_fhir_provider="550e8400-e29b-41d4-a716-446655440000:eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c...",
                 message="What is the patient's current condition?",
                 agent_id="agent-123",
             )
@@ -869,7 +899,13 @@ class AsyncAgentClient:
         asyncio.run(main())
         """
         _response = await self._raw_client.chat(
-            message=message, agent_id=agent_id, context=context, session_id=session_id, request_options=request_options
+            message=message,
+            agent_id=agent_id,
+            phenoml_on_behalf_of=phenoml_on_behalf_of,
+            phenoml_fhir_provider=phenoml_fhir_provider,
+            context=context,
+            session_id=session_id,
+            request_options=request_options,
         )
         return _response.data
 

phenoml/agent/raw_client.py

@@ -650,6 +650,8 @@ class RawAgentClient:
         *,
         message: str,
         agent_id: str,
+        phenoml_on_behalf_of: typing.Optional[str] = None,
+        phenoml_fhir_provider: typing.Optional[str] = None,
         context: typing.Optional[str] = OMIT,
         session_id: typing.Optional[str] = OMIT,
         request_options: typing.Optional[RequestOptions] = None,
@@ -665,6 +667,14 @@ class RawAgentClient:
         agent_id : str
             The ID of the agent to chat with
 
+        phenoml_on_behalf_of : typing.Optional[str]
+            Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
+            Must be in the format: Patient/{uuid} or Practitioner/{uuid}
+
+        phenoml_fhir_provider : typing.Optional[str]
+            Optional header for FHIR provider authentication. Contains credentials in the format {fhir_provider_id}:{oauth2_token}.
+            Multiple FHIR provider integrations can be provided as comma-separated values.
+
         context : typing.Optional[str]
             Optional context for the conversation
 
@@ -690,6 +700,8 @@ class RawAgentClient:
             },
             headers={
                 "content-type": "application/json",
+                "X-Phenoml-On-Behalf-Of": str(phenoml_on_behalf_of) if phenoml_on_behalf_of is not None else None,
+                "X-Phenoml-Fhir-Provider": str(phenoml_fhir_provider) if phenoml_fhir_provider is not None else None,
             },
             request_options=request_options,
             omit=OMIT,
@@ -1471,6 +1483,8 @@ class AsyncRawAgentClient:
         *,
         message: str,
         agent_id: str,
+        phenoml_on_behalf_of: typing.Optional[str] = None,
+        phenoml_fhir_provider: typing.Optional[str] = None,
         context: typing.Optional[str] = OMIT,
         session_id: typing.Optional[str] = OMIT,
         request_options: typing.Optional[RequestOptions] = None,
@@ -1486,6 +1500,14 @@ class AsyncRawAgentClient:
         agent_id : str
             The ID of the agent to chat with
 
+        phenoml_on_behalf_of : typing.Optional[str]
+            Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
+            Must be in the format: Patient/{uuid} or Practitioner/{uuid}
+
+        phenoml_fhir_provider : typing.Optional[str]
+            Optional header for FHIR provider authentication. Contains credentials in the format {fhir_provider_id}:{oauth2_token}.
+            Multiple FHIR provider integrations can be provided as comma-separated values.
+
         context : typing.Optional[str]
             Optional context for the conversation
 
@@ -1511,6 +1533,8 @@ class AsyncRawAgentClient:
             },
             headers={
                 "content-type": "application/json",
+                "X-Phenoml-On-Behalf-Of": str(phenoml_on_behalf_of) if phenoml_on_behalf_of is not None else None,
+                "X-Phenoml-Fhir-Provider": str(phenoml_fhir_provider) if phenoml_fhir_provider is not None else None,
             },
             request_options=request_options,
             omit=OMIT,

phenoml/client.py

@@ -35,7 +35,7 @@ class phenoml:
 
 
 
-    token : typing.Optional[typing.Union[str, typing.Callable[[], str]]]
+    token : typing.Union[str, typing.Callable[[], str]]
     headers : typing.Optional[typing.Dict[str, str]]
         Additional headers to send with every request.
 
@@ -62,7 +62,7 @@ class phenoml:
         *,
         base_url: typing.Optional[str] = None,
         environment: phenomlEnvironment = phenomlEnvironment.DEFAULT,
-        token: typing.Optional[typing.Union[str, typing.Callable[[], str]]] = None,
+        token: typing.Union[str, typing.Callable[[], str]],
         headers: typing.Optional[typing.Dict[str, str]] = None,
         timeout: typing.Optional[float] = None,
         follow_redirects: typing.Optional[bool] = True,
@@ -112,7 +112,7 @@ class Asyncphenoml:
 
 
 
-    token : typing.Optional[typing.Union[str, typing.Callable[[], str]]]
+    token : typing.Union[str, typing.Callable[[], str]]
     headers : typing.Optional[typing.Dict[str, str]]
         Additional headers to send with every request.
 
@@ -139,7 +139,7 @@ class Asyncphenoml:
         *,
         base_url: typing.Optional[str] = None,
         environment: phenomlEnvironment = phenomlEnvironment.DEFAULT,
-        token: typing.Optional[typing.Union[str, typing.Callable[[], str]]] = None,
+        token: typing.Union[str, typing.Callable[[], str]],
         headers: typing.Optional[typing.Dict[str, str]] = None,
         timeout: typing.Optional[float] = None,
         follow_redirects: typing.Optional[bool] = True,

phenoml/construe/__init__.py

@@ -3,43 +3,29 @@
 # isort: skip_file
 
 from .types import (
-    BadRequestErrorBody,
-    ConstrueCohortRequestConfig,
-    ConstrueCohortResponse,
-    ConstrueCohortResponseQueriesItem,
-    ConstrueCohortResponseQueriesItemCodeExtractResultsItem,
-    ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem,
     ConstrueUploadCodeSystemResponse,
     ExtractCodesResult,
     ExtractRequestConfig,
     ExtractRequestConfigChunkingMethod,
+    ExtractRequestConfigValidationMethod,
     ExtractRequestSystem,
     ExtractedCodeResult,
-    InternalServerErrorBody,
-    UnauthorizedErrorBody,
     UploadRequestFormat,
 )
 from .errors import BadRequestError, ConflictError, FailedDependencyError, InternalServerError, UnauthorizedError
 
 __all__ = [
     "BadRequestError",
-    "BadRequestErrorBody",
     "ConflictError",
-    "ConstrueCohortRequestConfig",
-    "ConstrueCohortResponse",
-    "ConstrueCohortResponseQueriesItem",
-    "ConstrueCohortResponseQueriesItemCodeExtractResultsItem",
-    "ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem",
     "ConstrueUploadCodeSystemResponse",
     "ExtractCodesResult",
     "ExtractRequestConfig",
     "ExtractRequestConfigChunkingMethod",
+    "ExtractRequestConfigValidationMethod",
     "ExtractRequestSystem",
     "ExtractedCodeResult",
     "FailedDependencyError",
     "InternalServerError",
-    "InternalServerErrorBody",
     "UnauthorizedError",
-    "UnauthorizedErrorBody",
     "UploadRequestFormat",
 ]

phenoml/construe/client.py

@@ -5,8 +5,6 @@ import typing
 from ..core.client_wrapper import AsyncClientWrapper, SyncClientWrapper
 from ..core.request_options import RequestOptions
 from .raw_client import AsyncRawConstrueClient, RawConstrueClient
-from .types.construe_cohort_request_config import ConstrueCohortRequestConfig
-from .types.construe_cohort_response import ConstrueCohortResponse
 from .types.construe_upload_code_system_response import ConstrueUploadCodeSystemResponse
 from .types.extract_codes_result import ExtractCodesResult
 from .types.extract_request_config import ExtractRequestConfig
@@ -155,46 +153,6 @@ class ConstrueClient:
         )
         return _response.data
 
-    def cohort(
-        self,
-        *,
-        text: str,
-        config: typing.Optional[ConstrueCohortRequestConfig] = OMIT,
-        request_options: typing.Optional[RequestOptions] = None,
-    ) -> ConstrueCohortResponse:
-        """
-        Creates a patient cohort based on a natural language description.
-        Translates the description into FHIR search queries and optional SQL queries.
-
-        Parameters
-        ----------
-        text : str
-            Natural language description of the desired patient cohort.
-
-        config : typing.Optional[ConstrueCohortRequestConfig]
-
-        request_options : typing.Optional[RequestOptions]
-            Request-specific configuration.
-
-        Returns
-        -------
-        ConstrueCohortResponse
-            Cohort creation successful
-
-        Examples
-        --------
-        from phenoml import phenoml
-
-        client = phenoml(
-            token="YOUR_TOKEN",
-        )
-        client.construe.cohort(
-            text="Between 20 and 40 years old with hyperlipidemia",
-        )
-        """
-        _response = self._raw_client.cohort(text=text, config=config, request_options=request_options)
-        return _response.data
-
 
 class AsyncConstrueClient:
     def __init__(self, *, client_wrapper: AsyncClientWrapper):
@@ -349,51 +307,3 @@ class AsyncConstrueClient:
             text=text, system=system, config=config, request_options=request_options
         )
         return _response.data
-
-    async def cohort(
-        self,
-        *,
-        text: str,
-        config: typing.Optional[ConstrueCohortRequestConfig] = OMIT,
-        request_options: typing.Optional[RequestOptions] = None,
-    ) -> ConstrueCohortResponse:
-        """
-        Creates a patient cohort based on a natural language description.
-        Translates the description into FHIR search queries and optional SQL queries.
-
-        Parameters
-        ----------
-        text : str
-            Natural language description of the desired patient cohort.
-
-        config : typing.Optional[ConstrueCohortRequestConfig]
-
-        request_options : typing.Optional[RequestOptions]
-            Request-specific configuration.
-
-        Returns
-        -------
-        ConstrueCohortResponse
-            Cohort creation successful
-
-        Examples
-        --------
-        import asyncio
-
-        from phenoml import Asyncphenoml
-
-        client = Asyncphenoml(
-            token="YOUR_TOKEN",
-        )
-
-
-        async def main() -> None:
-            await client.construe.cohort(
-                text="Between 20 and 40 years old with hyperlipidemia",
-            )
-
-
-        asyncio.run(main())
-        """
-        _response = await self._raw_client.cohort(text=text, config=config, request_options=request_options)
-        return _response.data

phenoml/construe/raw_client.py

@@ -14,8 +14,6 @@ from .errors.conflict_error import ConflictError
 from .errors.failed_dependency_error import FailedDependencyError
 from .errors.internal_server_error import InternalServerError
 from .errors.unauthorized_error import UnauthorizedError
-from .types.construe_cohort_request_config import ConstrueCohortRequestConfig
-from .types.construe_cohort_response import ConstrueCohortResponse
 from .types.construe_upload_code_system_response import ConstrueUploadCodeSystemResponse
 from .types.extract_codes_result import ExtractCodesResult
 from .types.extract_request_config import ExtractRequestConfig
@@ -276,95 +274,6 @@ class RawConstrueClient:
             raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response.text)
         raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response_json)
 
-    def cohort(
-        self,
-        *,
-        text: str,
-        config: typing.Optional[ConstrueCohortRequestConfig] = OMIT,
-        request_options: typing.Optional[RequestOptions] = None,
-    ) -> HttpResponse[ConstrueCohortResponse]:
-        """
-        Creates a patient cohort based on a natural language description.
-        Translates the description into FHIR search queries and optional SQL queries.
-
-        Parameters
-        ----------
-        text : str
-            Natural language description of the desired patient cohort.
-
-        config : typing.Optional[ConstrueCohortRequestConfig]
-
-        request_options : typing.Optional[RequestOptions]
-            Request-specific configuration.
-
-        Returns
-        -------
-        HttpResponse[ConstrueCohortResponse]
-            Cohort creation successful
-        """
-        _response = self._client_wrapper.httpx_client.request(
-            "construe/cohort",
-            method="POST",
-            json={
-                "config": convert_and_respect_annotation_metadata(
-                    object_=config, annotation=ConstrueCohortRequestConfig, direction="write"
-                ),
-                "text": text,
-            },
-            headers={
-                "content-type": "application/json",
-            },
-            request_options=request_options,
-            omit=OMIT,
-        )
-        try:
-            if 200 <= _response.status_code < 300:
-                _data = typing.cast(
-                    ConstrueCohortResponse,
-                    parse_obj_as(
-                        type_=ConstrueCohortResponse,  # type: ignore
-                        object_=_response.json(),
-                    ),
-                )
-                return HttpResponse(response=_response, data=_data)
-            if _response.status_code == 400:
-                raise BadRequestError(
-                    headers=dict(_response.headers),
-                    body=typing.cast(
-                        typing.Optional[typing.Any],
-                        parse_obj_as(
-                            type_=typing.Optional[typing.Any],  # type: ignore
-                            object_=_response.json(),
-                        ),
-                    ),
-                )
-            if _response.status_code == 401:
-                raise UnauthorizedError(
-                    headers=dict(_response.headers),
-                    body=typing.cast(
-                        typing.Optional[typing.Any],
-                        parse_obj_as(
-                            type_=typing.Optional[typing.Any],  # type: ignore
-                            object_=_response.json(),
-                        ),
-                    ),
-                )
-            if _response.status_code == 500:
-                raise InternalServerError(
-                    headers=dict(_response.headers),
-                    body=typing.cast(
-                        typing.Optional[typing.Any],
-                        parse_obj_as(
-                            type_=typing.Optional[typing.Any],  # type: ignore
-                            object_=_response.json(),
-                        ),
-                    ),
-                )
-            _response_json = _response.json()
-        except JSONDecodeError:
-            raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response.text)
-        raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response_json)
-
 
 class AsyncRawConstrueClient:
     def __init__(self, *, client_wrapper: AsyncClientWrapper):
@@ -615,92 +524,3 @@ class AsyncRawConstrueClient:
         except JSONDecodeError:
             raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response.text)
         raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response_json)
-
-    async def cohort(
-        self,
-        *,
-        text: str,
-        config: typing.Optional[ConstrueCohortRequestConfig] = OMIT,
-        request_options: typing.Optional[RequestOptions] = None,
-    ) -> AsyncHttpResponse[ConstrueCohortResponse]:
-        """
-        Creates a patient cohort based on a natural language description.
-        Translates the description into FHIR search queries and optional SQL queries.
-
-        Parameters
-        ----------
-        text : str
-            Natural language description of the desired patient cohort.
-
-        config : typing.Optional[ConstrueCohortRequestConfig]
-
-        request_options : typing.Optional[RequestOptions]
-            Request-specific configuration.
-
-        Returns
-        -------
-        AsyncHttpResponse[ConstrueCohortResponse]
-            Cohort creation successful
-        """
-        _response = await self._client_wrapper.httpx_client.request(
-            "construe/cohort",
-            method="POST",
-            json={
-                "config": convert_and_respect_annotation_metadata(
-                    object_=config, annotation=ConstrueCohortRequestConfig, direction="write"
-                ),
-                "text": text,
-            },
-            headers={
-                "content-type": "application/json",
-            },
-            request_options=request_options,
-            omit=OMIT,
-        )
-        try:
-            if 200 <= _response.status_code < 300:
-                _data = typing.cast(
-                    ConstrueCohortResponse,
-                    parse_obj_as(
-                        type_=ConstrueCohortResponse,  # type: ignore
-                        object_=_response.json(),
-                    ),
-                )
-                return AsyncHttpResponse(response=_response, data=_data)
-            if _response.status_code == 400:
-                raise BadRequestError(
-                    headers=dict(_response.headers),
-                    body=typing.cast(
-                        typing.Optional[typing.Any],
-                        parse_obj_as(
-                            type_=typing.Optional[typing.Any],  # type: ignore
-                            object_=_response.json(),
-                        ),
-                    ),
-                )
-            if _response.status_code == 401:
-                raise UnauthorizedError(
-                    headers=dict(_response.headers),
-                    body=typing.cast(
-                        typing.Optional[typing.Any],
-                        parse_obj_as(
-                            type_=typing.Optional[typing.Any],  # type: ignore
-                            object_=_response.json(),
-                        ),
-                    ),
-                )
-            if _response.status_code == 500:
-                raise InternalServerError(
-                    headers=dict(_response.headers),
-                    body=typing.cast(
-                        typing.Optional[typing.Any],
-                        parse_obj_as(
-                            type_=typing.Optional[typing.Any],  # type: ignore
-                            object_=_response.json(),
-                        ),
-                    ),
-                )
-            _response_json = _response.json()
-        except JSONDecodeError:
-            raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response.text)
-        raise ApiError(status_code=_response.status_code, headers=dict(_response.headers), body=_response_json)

phenoml/construe/types/__init__.py

@@ -2,40 +2,22 @@
 
 # isort: skip_file
 
-from .bad_request_error_body import BadRequestErrorBody
-from .construe_cohort_request_config import ConstrueCohortRequestConfig
-from .construe_cohort_response import ConstrueCohortResponse
-from .construe_cohort_response_queries_item import ConstrueCohortResponseQueriesItem
-from .construe_cohort_response_queries_item_code_extract_results_item import (
-    ConstrueCohortResponseQueriesItemCodeExtractResultsItem,
-)
-from .construe_cohort_response_queries_item_code_extract_results_item_codes_item import (
-    ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem,
-)
 from .construe_upload_code_system_response import ConstrueUploadCodeSystemResponse
 from .extract_codes_result import ExtractCodesResult
 from .extract_request_config import ExtractRequestConfig
 from .extract_request_config_chunking_method import ExtractRequestConfigChunkingMethod
+from .extract_request_config_validation_method import ExtractRequestConfigValidationMethod
 from .extract_request_system import ExtractRequestSystem
 from .extracted_code_result import ExtractedCodeResult
-from .internal_server_error_body import InternalServerErrorBody
-from .unauthorized_error_body import UnauthorizedErrorBody
 from .upload_request_format import UploadRequestFormat
 
 __all__ = [
-    "BadRequestErrorBody",
-    "ConstrueCohortRequestConfig",
-    "ConstrueCohortResponse",
-    "ConstrueCohortResponseQueriesItem",
-    "ConstrueCohortResponseQueriesItemCodeExtractResultsItem",
-    "ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem",
     "ConstrueUploadCodeSystemResponse",
     "ExtractCodesResult",
     "ExtractRequestConfig",
     "ExtractRequestConfigChunkingMethod",
+    "ExtractRequestConfigValidationMethod",
     "ExtractRequestSystem",
     "ExtractedCodeResult",
-    "InternalServerErrorBody",
-    "UnauthorizedErrorBody",
     "UploadRequestFormat",
 ]

phenoml/construe/types/extract_request_config.py

@@ -5,13 +5,42 @@ import typing
 import pydantic
 from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
 from .extract_request_config_chunking_method import ExtractRequestConfigChunkingMethod
+from .extract_request_config_validation_method import ExtractRequestConfigValidationMethod
 
 
 class ExtractRequestConfig(UniversalBaseModel):
-    chunking_method: typing.Optional[ExtractRequestConfigChunkingMethod] = None
-    max_codes_per_chunk: typing.Optional[int] = None
-    code_similarity_filter: typing.Optional[float] = None
-    include_rationale: typing.Optional[bool] = None
+    chunking_method: typing.Optional[ExtractRequestConfigChunkingMethod] = pydantic.Field(default=None)
+    """
+    Method for splitting input text into chunks before code extraction
+    """
+
+    max_codes_per_chunk: typing.Optional[int] = pydantic.Field(default=None)
+    """
+    Maximum number of codes to extract per chunk
+    """
+
+    code_similarity_filter: typing.Optional[float] = pydantic.Field(default=None)
+    """
+    Threshold for filtering similar codes (0.0-1.0)
+    """
+
+    validation_method: typing.Optional[ExtractRequestConfigValidationMethod] = pydantic.Field(default=None)
+    """
+    Method for validating extracted codes:
+    * none - No validation, returns all candidate codes
+    * simple - LLM-based validation
+    * medication_search - LLM-based validation tailored for medication concepts
+    """
+
+    include_rationale: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether to include explanations for why each code was extracted
+    """
+
+    include_ancestors: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether to include ancestor/parent codes in the results
+    """
 
     if IS_PYDANTIC_V2:
         model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2

phenoml/construe/types/extract_request_config_chunking_method.py

@@ -2,4 +2,6 @@
 
 import typing
 
-ExtractRequestConfigChunkingMethod = typing.Union[typing.Literal["none", "sentence", "paragraph", "topics"], typing.Any]
+ExtractRequestConfigChunkingMethod = typing.Union[
+    typing.Literal["none", "sentences", "paragraphs", "topics"], typing.Any
+]

phenoml/construe/types/extract_request_config_validation_method.py

@@ -0,0 +1,5 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+ExtractRequestConfigValidationMethod = typing.Union[typing.Literal["none", "simple", "medication_search"], typing.Any]

phenoml/construe/types/extract_request_system.py

@@ -17,6 +17,8 @@ class ExtractRequestSystem(UniversalBaseModel):
     * ICD-10-CM - version 2025
     * ICD-10-PCS - version 2025
     * LOINC - version 2.78
+    * HPO - version 2025
+    * CPT - version 2025
     
     Custom systems:
     * Any valid system name configured in your environment. Must have self-hosted construe module.