phenoml 0.0.6__py3-none-any.whl

phenoml/construe/client.py

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+# 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 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
+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 ConstrueClient:
+    def __init__(self, *, client_wrapper: SyncClientWrapper):
+        self._raw_client = RawConstrueClient(client_wrapper=client_wrapper)
+
+    @property
+    def with_raw_response(self) -> RawConstrueClient:
+        """
+        Retrieves a raw implementation of this client that returns raw responses.
+
+        Returns
+        -------
+        RawConstrueClient
+        """
+        return self._raw_client
+
+    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,
+    ) -> 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
+        -------
+        ConstrueUploadCodeSystemResponse
+            Successfully uploaded code system
+
+        Examples
+        --------
+        from phenoml import phenoml
+
+        client = phenoml(
+            token="YOUR_TOKEN",
+        )
+        client.construe.upload_code_system(
+            name="CUSTOM_CODES",
+            version="1.0",
+            format="json",
+            file="file",
+        )
+        """
+        _response = self._raw_client.upload_code_system(
+            name=name,
+            version=version,
+            format=format,
+            file=file,
+            revision=revision,
+            code_col=code_col,
+            desc_col=desc_col,
+            defn_col=defn_col,
+            request_options=request_options,
+        )
+        return _response.data
+
+    def extract_codes(
+        self,
+        *,
+        text: str,
+        system: typing.Optional[ExtractRequestSystem] = OMIT,
+        config: typing.Optional[ExtractRequestConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> 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
+        -------
+        ExtractCodesResult
+            Successfully extracted codes
+
+        Examples
+        --------
+        from phenoml import phenoml
+
+        client = phenoml(
+            token="YOUR_TOKEN",
+        )
+        client.construe.extract_codes(
+            text="Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney",
+        )
+        """
+        _response = self._raw_client.extract_codes(
+            text=text, system=system, config=config, request_options=request_options
+        )
+        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):
+        self._raw_client = AsyncRawConstrueClient(client_wrapper=client_wrapper)
+
+    @property
+    def with_raw_response(self) -> AsyncRawConstrueClient:
+        """
+        Retrieves a raw implementation of this client that returns raw responses.
+
+        Returns
+        -------
+        AsyncRawConstrueClient
+        """
+        return self._raw_client
+
+    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,
+    ) -> 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
+        -------
+        ConstrueUploadCodeSystemResponse
+            Successfully uploaded code system
+
+        Examples
+        --------
+        import asyncio
+
+        from phenoml import Asyncphenoml
+
+        client = Asyncphenoml(
+            token="YOUR_TOKEN",
+        )
+
+
+        async def main() -> None:
+            await client.construe.upload_code_system(
+                name="CUSTOM_CODES",
+                version="1.0",
+                format="json",
+                file="file",
+            )
+
+
+        asyncio.run(main())
+        """
+        _response = await self._raw_client.upload_code_system(
+            name=name,
+            version=version,
+            format=format,
+            file=file,
+            revision=revision,
+            code_col=code_col,
+            desc_col=desc_col,
+            defn_col=defn_col,
+            request_options=request_options,
+        )
+        return _response.data
+
+    async def extract_codes(
+        self,
+        *,
+        text: str,
+        system: typing.Optional[ExtractRequestSystem] = OMIT,
+        config: typing.Optional[ExtractRequestConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> 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
+        -------
+        ExtractCodesResult
+            Successfully extracted codes
+
+        Examples
+        --------
+        import asyncio
+
+        from phenoml import Asyncphenoml
+
+        client = Asyncphenoml(
+            token="YOUR_TOKEN",
+        )
+
+
+        async def main() -> None:
+            await client.construe.extract_codes(
+                text="Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney",
+            )
+
+
+        asyncio.run(main())
+        """
+        _response = await self._raw_client.extract_codes(
+            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/errors/__init__.py

@@ -0,0 +1,11 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .bad_request_error import BadRequestError
+from .conflict_error import ConflictError
+from .failed_dependency_error import FailedDependencyError
+from .internal_server_error import InternalServerError
+from .unauthorized_error import UnauthorizedError
+
+__all__ = ["BadRequestError", "ConflictError", "FailedDependencyError", "InternalServerError", "UnauthorizedError"]

phenoml/construe/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/construe/errors/conflict_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 ConflictError(ApiError):
+    def __init__(self, body: typing.Optional[typing.Any], headers: typing.Optional[typing.Dict[str, str]] = None):
+        super().__init__(status_code=409, headers=headers, body=body)

phenoml/construe/errors/failed_dependency_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 FailedDependencyError(ApiError):
+    def __init__(self, body: typing.Optional[typing.Any], headers: typing.Optional[typing.Dict[str, str]] = None):
+        super().__init__(status_code=424, headers=headers, body=body)

phenoml/construe/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/construe/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)