phenoml 0.0.6__py3-none-any.whl

phenoml/cohort/client.py

@@ -0,0 +1,113 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+from ..core.client_wrapper import AsyncClientWrapper, SyncClientWrapper
+from ..core.request_options import RequestOptions
+from .raw_client import AsyncRawCohortClient, RawCohortClient
+from .types.cohort_response import CohortResponse
+
+# this is used as the default value for optional parameters
+OMIT = typing.cast(typing.Any, ...)
+
+
+class CohortClient:
+    def __init__(self, *, client_wrapper: SyncClientWrapper):
+        self._raw_client = RawCohortClient(client_wrapper=client_wrapper)
+
+    @property
+    def with_raw_response(self) -> RawCohortClient:
+        """
+        Retrieves a raw implementation of this client that returns raw responses.
+
+        Returns
+        -------
+        RawCohortClient
+        """
+        return self._raw_client
+
+    def analyze(self, *, text: str, request_options: typing.Optional[RequestOptions] = None) -> CohortResponse:
+        """
+        Converts natural language text into structured FHIR search queries for patient cohort analysis
+
+        Parameters
+        ----------
+        text : str
+            Natural language text describing patient cohort criteria
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        CohortResponse
+            Successfully analyzed cohort criteria
+
+        Examples
+        --------
+        from phenoml import phenoml
+
+        client = phenoml(
+            token="YOUR_TOKEN",
+        )
+        client.cohort.analyze(
+            text="female patients over 65 with diabetes but not hypertension",
+        )
+        """
+        _response = self._raw_client.analyze(text=text, request_options=request_options)
+        return _response.data
+
+
+class AsyncCohortClient:
+    def __init__(self, *, client_wrapper: AsyncClientWrapper):
+        self._raw_client = AsyncRawCohortClient(client_wrapper=client_wrapper)
+
+    @property
+    def with_raw_response(self) -> AsyncRawCohortClient:
+        """
+        Retrieves a raw implementation of this client that returns raw responses.
+
+        Returns
+        -------
+        AsyncRawCohortClient
+        """
+        return self._raw_client
+
+    async def analyze(self, *, text: str, request_options: typing.Optional[RequestOptions] = None) -> CohortResponse:
+        """
+        Converts natural language text into structured FHIR search queries for patient cohort analysis
+
+        Parameters
+        ----------
+        text : str
+            Natural language text describing patient cohort criteria
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        CohortResponse
+            Successfully analyzed cohort criteria
+
+        Examples
+        --------
+        import asyncio
+
+        from phenoml import Asyncphenoml
+
+        client = Asyncphenoml(
+            token="YOUR_TOKEN",
+        )
+
+
+        async def main() -> None:
+            await client.cohort.analyze(
+                text="female patients over 65 with diabetes but not hypertension",
+            )
+
+
+        asyncio.run(main())
+        """
+        _response = await self._raw_client.analyze(text=text, request_options=request_options)
+        return _response.data

phenoml/cohort/errors/__init__.py

@@ -0,0 +1,9 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .bad_request_error import BadRequestError
+from .internal_server_error import InternalServerError
+from .unauthorized_error import UnauthorizedError
+
+__all__ = ["BadRequestError", "InternalServerError", "UnauthorizedError"]

phenoml/cohort/errors/bad_request_error.py

@@ -0,0 +1,10 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+from ...core.api_error import ApiError
+
+
+class BadRequestError(ApiError):
+    def __init__(self, body: typing.Optional[typing.Any], headers: typing.Optional[typing.Dict[str, str]] = None):
+        super().__init__(status_code=400, headers=headers, body=body)

phenoml/cohort/errors/internal_server_error.py

@@ -0,0 +1,10 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+from ...core.api_error import ApiError
+
+
+class InternalServerError(ApiError):
+    def __init__(self, body: typing.Optional[typing.Any], headers: typing.Optional[typing.Dict[str, str]] = None):
+        super().__init__(status_code=500, headers=headers, body=body)

phenoml/cohort/errors/unauthorized_error.py

@@ -0,0 +1,10 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+from ...core.api_error import ApiError
+
+
+class UnauthorizedError(ApiError):
+    def __init__(self, body: typing.Optional[typing.Any], headers: typing.Optional[typing.Dict[str, str]] = None):
+        super().__init__(status_code=401, headers=headers, body=body)

phenoml/cohort/raw_client.py

@@ -0,0 +1,185 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+from json.decoder import JSONDecodeError
+
+from ..core.api_error import ApiError
+from ..core.client_wrapper import AsyncClientWrapper, SyncClientWrapper
+from ..core.http_response import AsyncHttpResponse, HttpResponse
+from ..core.pydantic_utilities import parse_obj_as
+from ..core.request_options import RequestOptions
+from .errors.bad_request_error import BadRequestError
+from .errors.internal_server_error import InternalServerError
+from .errors.unauthorized_error import UnauthorizedError
+from .types.cohort_response import CohortResponse
+
+# this is used as the default value for optional parameters
+OMIT = typing.cast(typing.Any, ...)
+
+
+class RawCohortClient:
+    def __init__(self, *, client_wrapper: SyncClientWrapper):
+        self._client_wrapper = client_wrapper
+
+    def analyze(
+        self, *, text: str, request_options: typing.Optional[RequestOptions] = None
+    ) -> HttpResponse[CohortResponse]:
+        """
+        Converts natural language text into structured FHIR search queries for patient cohort analysis
+
+        Parameters
+        ----------
+        text : str
+            Natural language text describing patient cohort criteria
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        HttpResponse[CohortResponse]
+            Successfully analyzed cohort criteria
+        """
+        _response = self._client_wrapper.httpx_client.request(
+            "cohort",
+            method="POST",
+            json={
+                "text": text,
+            },
+            headers={
+                "content-type": "application/json",
+            },
+            request_options=request_options,
+            omit=OMIT,
+        )
+        try:
+            if 200 <= _response.status_code < 300:
+                _data = typing.cast(
+                    CohortResponse,
+                    parse_obj_as(
+                        type_=CohortResponse,  # 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 AsyncRawCohortClient:
+    def __init__(self, *, client_wrapper: AsyncClientWrapper):
+        self._client_wrapper = client_wrapper
+
+    async def analyze(
+        self, *, text: str, request_options: typing.Optional[RequestOptions] = None
+    ) -> AsyncHttpResponse[CohortResponse]:
+        """
+        Converts natural language text into structured FHIR search queries for patient cohort analysis
+
+        Parameters
+        ----------
+        text : str
+            Natural language text describing patient cohort criteria
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        AsyncHttpResponse[CohortResponse]
+            Successfully analyzed cohort criteria
+        """
+        _response = await self._client_wrapper.httpx_client.request(
+            "cohort",
+            method="POST",
+            json={
+                "text": text,
+            },
+            headers={
+                "content-type": "application/json",
+            },
+            request_options=request_options,
+            omit=OMIT,
+        )
+        try:
+            if 200 <= _response.status_code < 300:
+                _data = typing.cast(
+                    CohortResponse,
+                    parse_obj_as(
+                        type_=CohortResponse,  # 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/cohort/types/__init__.py

@@ -0,0 +1,8 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .cohort_response import CohortResponse
+from .search_concept import SearchConcept
+
+__all__ = ["CohortResponse", "SearchConcept"]

phenoml/cohort/types/cohort_response.py

@@ -0,0 +1,33 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from .search_concept import SearchConcept
+
+
+class CohortResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether the cohort analysis was successful
+    """
+
+    message: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Human-readable message about the analysis result
+    """
+
+    queries: typing.Optional[typing.List[SearchConcept]] = pydantic.Field(default=None)
+    """
+    Array of search concepts converted to FHIR search queries
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/cohort/types/search_concept.py

@@ -0,0 +1,37 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class SearchConcept(UniversalBaseModel):
+    resource_type: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    The FHIR resource type for this search concept
+    """
+
+    search_params: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    FHIR search parameters in standard format
+    """
+
+    concept: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    The original concept description
+    """
+
+    exclude: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether this concept should be excluded from the search
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/construe/__init__.py

@@ -0,0 +1,45 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .types import (
+    BadRequestErrorBody,
+    ConstrueCohortRequestConfig,
+    ConstrueCohortResponse,
+    ConstrueCohortResponseQueriesItem,
+    ConstrueCohortResponseQueriesItemCodeExtractResultsItem,
+    ConstrueCohortResponseQueriesItemCodeExtractResultsItemCodesItem,
+    ConstrueUploadCodeSystemResponse,
+    ExtractCodesResult,
+    ExtractRequestConfig,
+    ExtractRequestConfigChunkingMethod,
+    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",
+    "ExtractRequestSystem",
+    "ExtractedCodeResult",
+    "FailedDependencyError",
+    "InternalServerError",
+    "InternalServerErrorBody",
+    "UnauthorizedError",
+    "UnauthorizedErrorBody",
+    "UploadRequestFormat",
+]