phenoml 0.0.6__py3-none-any.whl

phenoml/construe/raw_client.py

@@ -0,0 +1,706 @@
+# 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 ..core.serialization import convert_and_respect_annotation_metadata
+from .errors.bad_request_error import BadRequestError
+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
+from .types.extract_request_system import ExtractRequestSystem
+from .types.upload_request_format import UploadRequestFormat
+
+# this is used as the default value for optional parameters
+OMIT = typing.cast(typing.Any, ...)
+
+
+class RawConstrueClient:
+    def __init__(self, *, client_wrapper: SyncClientWrapper):
+        self._client_wrapper = client_wrapper
+
+    def upload_code_system(
+        self,
+        *,
+        name: str,
+        version: str,
+        format: UploadRequestFormat,
+        file: str,
+        revision: typing.Optional[float] = OMIT,
+        code_col: typing.Optional[str] = OMIT,
+        desc_col: typing.Optional[str] = OMIT,
+        defn_col: typing.Optional[str] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> HttpResponse[ConstrueUploadCodeSystemResponse]:
+        """
+        Upload a custom medical code system with codes and descriptions for use in code extraction.
+        Upon upload, construe generates embeddings for all of the codes in the code system and stores them in the vector database so you can
+        subsequently use the code system for construe/extract and lang2fhir/create (coming soon!)
+
+        Parameters
+        ----------
+        name : str
+            Name of the code system
+
+        version : str
+            Version of the code system
+
+        format : UploadRequestFormat
+            Format of the uploaded file
+
+        file : str
+            The file contents as a base64-encoded string
+
+        revision : typing.Optional[float]
+            Optional revision number
+
+        code_col : typing.Optional[str]
+            Column name containing codes (required for CSV format)
+
+        desc_col : typing.Optional[str]
+            Column name containing descriptions (required for CSV format)
+
+        defn_col : typing.Optional[str]
+            Optional column name containing long definitions (for CSV format)
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        HttpResponse[ConstrueUploadCodeSystemResponse]
+            Successfully uploaded code system
+        """
+        _response = self._client_wrapper.httpx_client.request(
+            "construe/upload",
+            method="POST",
+            json={
+                "name": name,
+                "version": version,
+                "revision": revision,
+                "format": format,
+                "file": file,
+                "code_col": code_col,
+                "desc_col": desc_col,
+                "defn_col": defn_col,
+            },
+            headers={
+                "content-type": "application/json",
+            },
+            request_options=request_options,
+            omit=OMIT,
+        )
+        try:
+            if 200 <= _response.status_code < 300:
+                _data = typing.cast(
+                    ConstrueUploadCodeSystemResponse,
+                    parse_obj_as(
+                        type_=ConstrueUploadCodeSystemResponse,  # 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 == 409:
+                raise ConflictError(
+                    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 == 424:
+                raise FailedDependencyError(
+                    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)
+
+    def extract_codes(
+        self,
+        *,
+        text: str,
+        system: typing.Optional[ExtractRequestSystem] = OMIT,
+        config: typing.Optional[ExtractRequestConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> HttpResponse[ExtractCodesResult]:
+        """
+        Converts natural language text into structured medical codes
+
+        Parameters
+        ----------
+        text : str
+            Natural language text to extract codes from
+
+        system : typing.Optional[ExtractRequestSystem]
+
+        config : typing.Optional[ExtractRequestConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        HttpResponse[ExtractCodesResult]
+            Successfully extracted codes
+        """
+        _response = self._client_wrapper.httpx_client.request(
+            "construe/extract",
+            method="POST",
+            json={
+                "text": text,
+                "system": convert_and_respect_annotation_metadata(
+                    object_=system, annotation=ExtractRequestSystem, direction="write"
+                ),
+                "config": convert_and_respect_annotation_metadata(
+                    object_=config, annotation=ExtractRequestConfig, direction="write"
+                ),
+            },
+            headers={
+                "content-type": "application/json",
+            },
+            request_options=request_options,
+            omit=OMIT,
+        )
+        try:
+            if 200 <= _response.status_code < 300:
+                _data = typing.cast(
+                    ExtractCodesResult,
+                    parse_obj_as(
+                        type_=ExtractCodesResult,  # 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 == 424:
+                raise FailedDependencyError(
+                    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)
+
+    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):
+        self._client_wrapper = client_wrapper
+
+    async def upload_code_system(
+        self,
+        *,
+        name: str,
+        version: str,
+        format: UploadRequestFormat,
+        file: str,
+        revision: typing.Optional[float] = OMIT,
+        code_col: typing.Optional[str] = OMIT,
+        desc_col: typing.Optional[str] = OMIT,
+        defn_col: typing.Optional[str] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> AsyncHttpResponse[ConstrueUploadCodeSystemResponse]:
+        """
+        Upload a custom medical code system with codes and descriptions for use in code extraction.
+        Upon upload, construe generates embeddings for all of the codes in the code system and stores them in the vector database so you can
+        subsequently use the code system for construe/extract and lang2fhir/create (coming soon!)
+
+        Parameters
+        ----------
+        name : str
+            Name of the code system
+
+        version : str
+            Version of the code system
+
+        format : UploadRequestFormat
+            Format of the uploaded file
+
+        file : str
+            The file contents as a base64-encoded string
+
+        revision : typing.Optional[float]
+            Optional revision number
+
+        code_col : typing.Optional[str]
+            Column name containing codes (required for CSV format)
+
+        desc_col : typing.Optional[str]
+            Column name containing descriptions (required for CSV format)
+
+        defn_col : typing.Optional[str]
+            Optional column name containing long definitions (for CSV format)
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        AsyncHttpResponse[ConstrueUploadCodeSystemResponse]
+            Successfully uploaded code system
+        """
+        _response = await self._client_wrapper.httpx_client.request(
+            "construe/upload",
+            method="POST",
+            json={
+                "name": name,
+                "version": version,
+                "revision": revision,
+                "format": format,
+                "file": file,
+                "code_col": code_col,
+                "desc_col": desc_col,
+                "defn_col": defn_col,
+            },
+            headers={
+                "content-type": "application/json",
+            },
+            request_options=request_options,
+            omit=OMIT,
+        )
+        try:
+            if 200 <= _response.status_code < 300:
+                _data = typing.cast(
+                    ConstrueUploadCodeSystemResponse,
+                    parse_obj_as(
+                        type_=ConstrueUploadCodeSystemResponse,  # 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 == 409:
+                raise ConflictError(
+                    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 == 424:
+                raise FailedDependencyError(
+                    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)
+
+    async def extract_codes(
+        self,
+        *,
+        text: str,
+        system: typing.Optional[ExtractRequestSystem] = OMIT,
+        config: typing.Optional[ExtractRequestConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> AsyncHttpResponse[ExtractCodesResult]:
+        """
+        Converts natural language text into structured medical codes
+
+        Parameters
+        ----------
+        text : str
+            Natural language text to extract codes from
+
+        system : typing.Optional[ExtractRequestSystem]
+
+        config : typing.Optional[ExtractRequestConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        AsyncHttpResponse[ExtractCodesResult]
+            Successfully extracted codes
+        """
+        _response = await self._client_wrapper.httpx_client.request(
+            "construe/extract",
+            method="POST",
+            json={
+                "text": text,
+                "system": convert_and_respect_annotation_metadata(
+                    object_=system, annotation=ExtractRequestSystem, direction="write"
+                ),
+                "config": convert_and_respect_annotation_metadata(
+                    object_=config, annotation=ExtractRequestConfig, direction="write"
+                ),
+            },
+            headers={
+                "content-type": "application/json",
+            },
+            request_options=request_options,
+            omit=OMIT,
+        )
+        try:
+            if 200 <= _response.status_code < 300:
+                _data = typing.cast(
+                    ExtractCodesResult,
+                    parse_obj_as(
+                        type_=ExtractCodesResult,  # 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 == 424:
+                raise FailedDependencyError(
+                    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)
+
+    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)