phenoml 0.0.1__py3-none-any.whl

phenoml/lang2fhir/types/__init__.py

@@ -0,0 +1,19 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .create_request_resource import CreateRequestResource
+from .document_request_file_type import DocumentRequestFileType
+from .document_request_resource import DocumentRequestResource
+from .fhir_resource import FhirResource
+from .lang2fhir_upload_profile_response import Lang2FhirUploadProfileResponse
+from .search_response import SearchResponse
+
+__all__ = [
+    "CreateRequestResource",
+    "DocumentRequestFileType",
+    "DocumentRequestResource",
+    "FhirResource",
+    "Lang2FhirUploadProfileResponse",
+    "SearchResponse",
+]

phenoml/lang2fhir/types/create_request_resource.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+CreateRequestResource = typing.Union[
+    typing.Literal[
+        "auto",
+        "appointment",
+        "condition-encounter-diagnosis",
+        "medicationrequest",
+        "careplan",
+        "condition-problems-health-concerns",
+        "coverage",
+        "encounter",
+        "observation-clinical-result",
+        "observation-lab",
+        "patient",
+        "procedure",
+        "questionnaire",
+        "questionnaireresponse",
+        "simple-observation",
+        "vital-signs",
+    ],
+    typing.Any,
+]

phenoml/lang2fhir/types/document_request_file_type.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+DocumentRequestFileType = typing.Union[
+    typing.Literal["application/pdf", "image/png", "image/jpeg", "image/jpg"], typing.Any
+]

phenoml/lang2fhir/types/document_request_resource.py

@@ -0,0 +1,5 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+DocumentRequestResource = typing.Union[typing.Literal["questionnaire", "questionnaireresponse"], typing.Any]

phenoml/lang2fhir/types/fhir_resource.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+FhirResource = typing.Dict[str, typing.Optional[typing.Any]]

phenoml/lang2fhir/types/lang2fhir_upload_profile_response.py

@@ -0,0 +1,23 @@
+# 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 Lang2FhirUploadProfileResponse(UniversalBaseModel):
+    message: typing.Optional[str] = None
+    id: typing.Optional[str] = None
+    resource: typing.Optional[str] = None
+    version: typing.Optional[str] = None
+    url: typing.Optional[str] = None
+
+    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/lang2fhir/types/search_response.py

@@ -0,0 +1,33 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+import typing_extensions
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from ...core.serialization import FieldMetadata
+
+
+class SearchResponse(UniversalBaseModel):
+    resource_type: typing_extensions.Annotated[typing.Optional[str], FieldMetadata(alias="resourceType")] = (
+        pydantic.Field(default=None)
+    )
+    """
+    The FHIR resource type identified for the search
+    """
+
+    search_params: typing_extensions.Annotated[typing.Optional[str], FieldMetadata(alias="searchParams")] = (
+        pydantic.Field(default=None)
+    )
+    """
+    FHIR search parameters in standard format
+    """
+
+    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/tools/__init__.py

@@ -0,0 +1,33 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .types import (
+    CohortRequestProvider,
+    CohortResponse,
+    FhirClientConfig,
+    Lang2FhirAndCreateRequestProvider,
+    Lang2FhirAndCreateRequestResource,
+    Lang2FhirAndCreateResponse,
+    Lang2FhirAndSearchRequestProvider,
+    Lang2FhirAndSearchResponse,
+    SearchConcept,
+)
+from .errors import BadRequestError, FailedDependencyError, ForbiddenError, InternalServerError, UnauthorizedError
+
+__all__ = [
+    "BadRequestError",
+    "CohortRequestProvider",
+    "CohortResponse",
+    "FailedDependencyError",
+    "FhirClientConfig",
+    "ForbiddenError",
+    "InternalServerError",
+    "Lang2FhirAndCreateRequestProvider",
+    "Lang2FhirAndCreateRequestResource",
+    "Lang2FhirAndCreateResponse",
+    "Lang2FhirAndSearchRequestProvider",
+    "Lang2FhirAndSearchResponse",
+    "SearchConcept",
+    "UnauthorizedError",
+]

phenoml/tools/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 AsyncRawToolsClient, RawToolsClient
+from .types.cohort_request_provider import CohortRequestProvider
+from .types.cohort_response import CohortResponse
+from .types.fhir_client_config import FhirClientConfig
+from .types.lang2fhir_and_create_request_provider import Lang2FhirAndCreateRequestProvider
+from .types.lang2fhir_and_create_request_resource import Lang2FhirAndCreateRequestResource
+from .types.lang2fhir_and_create_response import Lang2FhirAndCreateResponse
+from .types.lang2fhir_and_search_request_provider import Lang2FhirAndSearchRequestProvider
+from .types.lang2fhir_and_search_response import Lang2FhirAndSearchResponse
+
+# this is used as the default value for optional parameters
+OMIT = typing.cast(typing.Any, ...)
+
+
+class ToolsClient:
+    def __init__(self, *, client_wrapper: SyncClientWrapper):
+        self._raw_client = RawToolsClient(client_wrapper=client_wrapper)
+
+    @property
+    def with_raw_response(self) -> RawToolsClient:
+        """
+        Retrieves a raw implementation of this client that returns raw responses.
+
+        Returns
+        -------
+        RawToolsClient
+        """
+        return self._raw_client
+
+    def create_fhir_resource(
+        self,
+        *,
+        resource: Lang2FhirAndCreateRequestResource,
+        text: str,
+        provider: typing.Optional[Lang2FhirAndCreateRequestProvider] = OMIT,
+        meta: typing.Optional[FhirClientConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> Lang2FhirAndCreateResponse:
+        """
+        Converts natural language to FHIR resource and optionally stores it in a FHIR server
+
+        Parameters
+        ----------
+        resource : Lang2FhirAndCreateRequestResource
+            Type of FHIR resource to create. Use 'auto' for automatic resource type detection, or specify a supported US Core profile.
+
+        text : str
+            Natural language text to convert to FHIR resource
+
+        provider : typing.Optional[Lang2FhirAndCreateRequestProvider]
+            FHIR provider to use for storing the resource
+
+        meta : typing.Optional[FhirClientConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        Lang2FhirAndCreateResponse
+            Successfully created FHIR resource
+
+        Examples
+        --------
+        from phenoml import phenoml
+
+        client = phenoml(
+            token="YOUR_TOKEN",
+        )
+        client.tools.create_fhir_resource(
+            resource="auto",
+            text="Patient John Doe has severe asthma with acute exacerbation",
+        )
+        """
+        _response = self._raw_client.create_fhir_resource(
+            resource=resource, text=text, provider=provider, meta=meta, request_options=request_options
+        )
+        return _response.data
+
+    def search_fhir_resources(
+        self,
+        *,
+        text: str,
+        patient_id: typing.Optional[str] = OMIT,
+        practitioner_id: typing.Optional[str] = OMIT,
+        count: typing.Optional[int] = OMIT,
+        provider: typing.Optional[Lang2FhirAndSearchRequestProvider] = OMIT,
+        meta: typing.Optional[FhirClientConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> Lang2FhirAndSearchResponse:
+        """
+        Converts natural language to FHIR search parameters and executes search in FHIR server
+
+        Parameters
+        ----------
+        text : str
+            Natural language text to convert to FHIR search parameters
+
+        patient_id : typing.Optional[str]
+            Patient ID to filter results
+
+        practitioner_id : typing.Optional[str]
+            Practitioner ID to filter results
+
+        count : typing.Optional[int]
+            Maximum number of results to return
+
+        provider : typing.Optional[Lang2FhirAndSearchRequestProvider]
+            FHIR provider to use for searching
+
+        meta : typing.Optional[FhirClientConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        Lang2FhirAndSearchResponse
+            Successfully generated search and retrieved results
+
+        Examples
+        --------
+        from phenoml import phenoml
+
+        client = phenoml(
+            token="YOUR_TOKEN",
+        )
+        client.tools.search_fhir_resources(
+            text="Find all appointments for patient John Doe next week",
+        )
+        """
+        _response = self._raw_client.search_fhir_resources(
+            text=text,
+            patient_id=patient_id,
+            practitioner_id=practitioner_id,
+            count=count,
+            provider=provider,
+            meta=meta,
+            request_options=request_options,
+        )
+        return _response.data
+
+    def analyze_cohort(
+        self,
+        *,
+        text: str,
+        provider: CohortRequestProvider,
+        meta: typing.Optional[FhirClientConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> CohortResponse:
+        """
+        Uses LLM to extract search concepts from natural language and builds patient cohorts with inclusion/exclusion criteria
+
+        Parameters
+        ----------
+        text : str
+            Natural language text describing the patient cohort criteria
+
+        provider : CohortRequestProvider
+            FHIR provider to use for searching
+
+        meta : typing.Optional[FhirClientConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        CohortResponse
+            Successfully analyzed cohort and retrieved patient list
+
+        Examples
+        --------
+        from phenoml import phenoml
+
+        client = phenoml(
+            token="YOUR_TOKEN",
+        )
+        client.tools.analyze_cohort(
+            text="female patients over 20 with diabetes but not hypertension",
+            provider="medplum",
+        )
+        """
+        _response = self._raw_client.analyze_cohort(
+            text=text, provider=provider, meta=meta, request_options=request_options
+        )
+        return _response.data
+
+
+class AsyncToolsClient:
+    def __init__(self, *, client_wrapper: AsyncClientWrapper):
+        self._raw_client = AsyncRawToolsClient(client_wrapper=client_wrapper)
+
+    @property
+    def with_raw_response(self) -> AsyncRawToolsClient:
+        """
+        Retrieves a raw implementation of this client that returns raw responses.
+
+        Returns
+        -------
+        AsyncRawToolsClient
+        """
+        return self._raw_client
+
+    async def create_fhir_resource(
+        self,
+        *,
+        resource: Lang2FhirAndCreateRequestResource,
+        text: str,
+        provider: typing.Optional[Lang2FhirAndCreateRequestProvider] = OMIT,
+        meta: typing.Optional[FhirClientConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> Lang2FhirAndCreateResponse:
+        """
+        Converts natural language to FHIR resource and optionally stores it in a FHIR server
+
+        Parameters
+        ----------
+        resource : Lang2FhirAndCreateRequestResource
+            Type of FHIR resource to create. Use 'auto' for automatic resource type detection, or specify a supported US Core profile.
+
+        text : str
+            Natural language text to convert to FHIR resource
+
+        provider : typing.Optional[Lang2FhirAndCreateRequestProvider]
+            FHIR provider to use for storing the resource
+
+        meta : typing.Optional[FhirClientConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        Lang2FhirAndCreateResponse
+            Successfully created FHIR resource
+
+        Examples
+        --------
+        import asyncio
+
+        from phenoml import Asyncphenoml
+
+        client = Asyncphenoml(
+            token="YOUR_TOKEN",
+        )
+
+
+        async def main() -> None:
+            await client.tools.create_fhir_resource(
+                resource="auto",
+                text="Patient John Doe has severe asthma with acute exacerbation",
+            )
+
+
+        asyncio.run(main())
+        """
+        _response = await self._raw_client.create_fhir_resource(
+            resource=resource, text=text, provider=provider, meta=meta, request_options=request_options
+        )
+        return _response.data
+
+    async def search_fhir_resources(
+        self,
+        *,
+        text: str,
+        patient_id: typing.Optional[str] = OMIT,
+        practitioner_id: typing.Optional[str] = OMIT,
+        count: typing.Optional[int] = OMIT,
+        provider: typing.Optional[Lang2FhirAndSearchRequestProvider] = OMIT,
+        meta: typing.Optional[FhirClientConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> Lang2FhirAndSearchResponse:
+        """
+        Converts natural language to FHIR search parameters and executes search in FHIR server
+
+        Parameters
+        ----------
+        text : str
+            Natural language text to convert to FHIR search parameters
+
+        patient_id : typing.Optional[str]
+            Patient ID to filter results
+
+        practitioner_id : typing.Optional[str]
+            Practitioner ID to filter results
+
+        count : typing.Optional[int]
+            Maximum number of results to return
+
+        provider : typing.Optional[Lang2FhirAndSearchRequestProvider]
+            FHIR provider to use for searching
+
+        meta : typing.Optional[FhirClientConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        Lang2FhirAndSearchResponse
+            Successfully generated search and retrieved results
+
+        Examples
+        --------
+        import asyncio
+
+        from phenoml import Asyncphenoml
+
+        client = Asyncphenoml(
+            token="YOUR_TOKEN",
+        )
+
+
+        async def main() -> None:
+            await client.tools.search_fhir_resources(
+                text="Find all appointments for patient John Doe next week",
+            )
+
+
+        asyncio.run(main())
+        """
+        _response = await self._raw_client.search_fhir_resources(
+            text=text,
+            patient_id=patient_id,
+            practitioner_id=practitioner_id,
+            count=count,
+            provider=provider,
+            meta=meta,
+            request_options=request_options,
+        )
+        return _response.data
+
+    async def analyze_cohort(
+        self,
+        *,
+        text: str,
+        provider: CohortRequestProvider,
+        meta: typing.Optional[FhirClientConfig] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> CohortResponse:
+        """
+        Uses LLM to extract search concepts from natural language and builds patient cohorts with inclusion/exclusion criteria
+
+        Parameters
+        ----------
+        text : str
+            Natural language text describing the patient cohort criteria
+
+        provider : CohortRequestProvider
+            FHIR provider to use for searching
+
+        meta : typing.Optional[FhirClientConfig]
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        CohortResponse
+            Successfully analyzed cohort and retrieved patient list
+
+        Examples
+        --------
+        import asyncio
+
+        from phenoml import Asyncphenoml
+
+        client = Asyncphenoml(
+            token="YOUR_TOKEN",
+        )
+
+
+        async def main() -> None:
+            await client.tools.analyze_cohort(
+                text="female patients over 20 with diabetes but not hypertension",
+                provider="medplum",
+            )
+
+
+        asyncio.run(main())
+        """
+        _response = await self._raw_client.analyze_cohort(
+            text=text, provider=provider, meta=meta, request_options=request_options
+        )
+        return _response.data

phenoml/tools/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 .failed_dependency_error import FailedDependencyError
+from .forbidden_error import ForbiddenError
+from .internal_server_error import InternalServerError
+from .unauthorized_error import UnauthorizedError
+
+__all__ = ["BadRequestError", "FailedDependencyError", "ForbiddenError", "InternalServerError", "UnauthorizedError"]

phenoml/tools/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/tools/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/tools/errors/forbidden_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 ForbiddenError(ApiError):
+    def __init__(self, body: typing.Optional[typing.Any], headers: typing.Optional[typing.Dict[str, str]] = None):
+        super().__init__(status_code=403, headers=headers, body=body)

phenoml/tools/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/tools/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)