phenoml 0.0.2__py3-none-any.whl → 0.0.17__py3-none-any.whl

phenoml/fhir_provider/types/__init__.py

@@ -0,0 +1,37 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .auth_method import AuthMethod
+from .fhir_provider_auth_config import FhirProviderAuthConfig
+from .fhir_provider_delete_response import FhirProviderDeleteResponse
+from .fhir_provider_list_response import FhirProviderListResponse
+from .fhir_provider_remove_auth_config_response import FhirProviderRemoveAuthConfigResponse
+from .fhir_provider_response import FhirProviderResponse
+from .fhir_provider_set_active_auth_config_response import FhirProviderSetActiveAuthConfigResponse
+from .fhir_provider_template import FhirProviderTemplate
+from .fhir_query_response import FhirQueryResponse
+from .fhir_query_response_data import FhirQueryResponseData
+from .json_web_key import JsonWebKey
+from .provider import Provider
+from .role import Role
+from .service_account_key import ServiceAccountKey
+from .smart_configuration import SmartConfiguration
+
+__all__ = [
+    "AuthMethod",
+    "FhirProviderAuthConfig",
+    "FhirProviderDeleteResponse",
+    "FhirProviderListResponse",
+    "FhirProviderRemoveAuthConfigResponse",
+    "FhirProviderResponse",
+    "FhirProviderSetActiveAuthConfigResponse",
+    "FhirProviderTemplate",
+    "FhirQueryResponse",
+    "FhirQueryResponseData",
+    "JsonWebKey",
+    "Provider",
+    "Role",
+    "ServiceAccountKey",
+    "SmartConfiguration",
+]

phenoml/fhir_provider/types/auth_method.py

@@ -0,0 +1,7 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+AuthMethod = typing.Union[
+    typing.Literal["client_secret", "google_healthcare", "jwt", "on_behalf_of", "token_passthrough", "none"], typing.Any
+]

phenoml/fhir_provider/types/fhir_provider_auth_config.py

@@ -0,0 +1,53 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import datetime as dt
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from .auth_method import AuthMethod
+from .json_web_key import JsonWebKey
+from .smart_configuration import SmartConfiguration
+
+
+class FhirProviderAuthConfig(UniversalBaseModel):
+    """
+    Authentication configuration for a FHIR provider (sensitive fields are hidden from JSON responses)
+    """
+
+    auth_config_id: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Unique identifier for this auth configuration
+    """
+
+    auth_method: typing.Optional[AuthMethod] = None
+    is_active_auth_config: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether this auth configuration is currently active
+    """
+
+    public_key_cert_pem: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Public key certificate in PEM format (visible for JWT auth)
+    """
+
+    json_web_key: typing.Optional[JsonWebKey] = None
+    credential_expiry: typing.Optional[dt.datetime] = pydantic.Field(default=None)
+    """
+    Expiry time for credentials (JWT auth only)
+    """
+
+    smart_configuration: typing.Optional[SmartConfiguration] = None
+    scopes: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    OAuth scopes
+    """
+
+    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/fhir_provider/types/fhir_provider_delete_response.py

@@ -0,0 +1,20 @@
+# 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 FhirProviderDeleteResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = None
+    message: 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/fhir_provider/types/fhir_provider_list_response.py

@@ -0,0 +1,22 @@
+# 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 .fhir_provider_template import FhirProviderTemplate
+
+
+class FhirProviderListResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = None
+    message: typing.Optional[str] = None
+    fhir_providers: typing.Optional[typing.List[FhirProviderTemplate]] = 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/fhir_provider/types/fhir_provider_remove_auth_config_response.py

@@ -0,0 +1,22 @@
+# 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 .fhir_provider_template import FhirProviderTemplate
+
+
+class FhirProviderRemoveAuthConfigResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = None
+    message: typing.Optional[str] = None
+    data: typing.Optional[FhirProviderTemplate] = 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/fhir_provider/types/fhir_provider_response.py

@@ -0,0 +1,22 @@
+# 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 .fhir_provider_template import FhirProviderTemplate
+
+
+class FhirProviderResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = None
+    message: typing.Optional[str] = None
+    data: typing.Optional[FhirProviderTemplate] = 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/fhir_provider/types/fhir_provider_set_active_auth_config_response.py

@@ -0,0 +1,22 @@
+# 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 .fhir_provider_template import FhirProviderTemplate
+
+
+class FhirProviderSetActiveAuthConfigResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = None
+    message: typing.Optional[str] = None
+    data: typing.Optional[FhirProviderTemplate] = 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/fhir_provider/types/fhir_provider_template.py

@@ -0,0 +1,66 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import datetime as dt
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from .fhir_provider_auth_config import FhirProviderAuthConfig
+from .provider import Provider
+
+
+class FhirProviderTemplate(UniversalBaseModel):
+    id: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Unique identifier for the FHIR provider
+    """
+
+    user_id: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    ID of the user who owns this FHIR provider
+    """
+
+    name: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Display name for the FHIR provider
+    """
+
+    description: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Optional description of the FHIR provider
+    """
+
+    provider: typing.Optional[Provider] = None
+    base_url: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Base URL of the FHIR server
+    """
+
+    client_id: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    OAuth client ID
+    """
+
+    auth_configs: typing.Optional[typing.Dict[str, FhirProviderAuthConfig]] = pydantic.Field(default=None)
+    """
+    Map of authentication configurations (key is auth_config_id)
+    """
+
+    is_active: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether the FHIR provider is active
+    """
+
+    last_updated: typing.Optional[dt.datetime] = pydantic.Field(default=None)
+    """
+    Timestamp when the provider was last updated
+    """
+
+    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/fhir_provider/types/fhir_query_response.py

@@ -0,0 +1,27 @@
+# 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 .fhir_query_response_data import FhirQueryResponseData
+
+
+class FhirQueryResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = None
+    status: typing.Optional[int] = pydantic.Field(default=None)
+    """
+    HTTP status code from the FHIR server response
+    """
+
+    message: typing.Optional[str] = None
+    data: typing.Optional[FhirQueryResponseData] = 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/fhir_provider/types/fhir_query_response_data.py

@@ -0,0 +1,5 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+FhirQueryResponseData = typing.Union[typing.Dict[str, typing.Optional[typing.Any]], str]

phenoml/fhir_provider/types/json_web_key.py

@@ -0,0 +1,51 @@
+# 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 JsonWebKey(UniversalBaseModel):
+    """
+    JSON Web Key structure for RSA keys used in JWT authentication. Keys are automatically generated using RSA-2048 with RS384 signing algorithm. The Key ID (kid) is derived from a SHA256 hash of the public key PEM format.
+    """
+
+    kty: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Key Type
+    """
+
+    use: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Usage (sig for signature)
+    """
+
+    kid: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Key ID - SHA256 hash of the public key PEM (including headers) encoded as base64url. Generated by taking the public key in PEM format, hashing with SHA256, then base64url encoding (replacing + with -, / with _, and removing padding).
+    """
+
+    alg: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Algorithm used for JWT signing (RSA with SHA-384)
+    """
+
+    n: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    RSA Modulus (base64url encoded)
+    """
+
+    e: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    RSA Exponent (base64url encoded)
+    """
+
+    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/fhir_provider/types/provider.py

@@ -0,0 +1,8 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+Provider = typing.Union[
+    typing.Literal["athenahealth", "canvas", "cerner", "elation", "epic", "google_healthcare", "hapi", "medplum"],
+    typing.Any,
+]

phenoml/fhir_provider/types/role.py

@@ -0,0 +1,27 @@
+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+Role = typing.Union[
+    typing.Literal[
+        "SmartV1Admin",
+        "SmartV1Read",
+        "SmartV1Write",
+        "SmartV2Admin",
+        "SmartV2Read",
+        "SmartV2Write",
+        "USCDISmartV1Admin",
+        "USCDISmartV1Read",
+        "USCDISmartV1Write",
+        "USCDISmartV2Admin",
+        "USCDISmartV2Read",
+        "USCDISmartV2Write",
+        "CernerSmartV1Admin",
+        "CernerSmartV1Read",
+        "CernerSmartV1Write",
+        "CernerSmartV2Admin",
+        "CernerSmartV2Read",
+        "CernerSmartV2Write",
+    ],
+    typing.Any,
+]

phenoml/fhir_provider/types/service_account_key.py

@@ -0,0 +1,35 @@
+# 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 ServiceAccountKey(UniversalBaseModel):
+    """
+    Google Cloud Service Account key (required for google_healthcare auth method)
+    """
+
+    type: str
+    project_id: str
+    private_key_id: str
+    private_key: str
+    client_email: str
+    client_id: str
+    auth_uri: str
+    token_uri: str
+    auth_provider_x509cert_url: typing_extensions.Annotated[str, FieldMetadata(alias="auth_provider_x509_cert_url")]
+    client_x509cert_url: typing_extensions.Annotated[str, FieldMetadata(alias="client_x509_cert_url")]
+    universe_domain: str
+
+    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/fhir_provider/types/smart_configuration.py

@@ -0,0 +1,46 @@
+# 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 SmartConfiguration(UniversalBaseModel):
+    """
+    SMART on FHIR configuration for OAuth-based providers
+    """
+
+    authorization_endpoint: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    OAuth2 authorization endpoint
+    """
+
+    token_endpoint: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    OAuth2 token endpoint
+    """
+
+    issuer: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    OIDC issuer URL
+    """
+
+    jwks_uri: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    JSON Web Key Set URI
+    """
+
+    scopes_supported: typing.Optional[typing.List[str]] = pydantic.Field(default=None)
+    """
+    List of supported scopes
+    """
+
+    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/__init__.py

@@ -3,6 +3,11 @@
 # isort: skip_file
 
 from .types import (
+    CreateMultiResponse,
+    CreateMultiResponseBundle,
+    CreateMultiResponseBundleEntryItem,
+    CreateMultiResponseBundleEntryItemRequest,
+    CreateMultiResponseResourcesItem,
     CreateRequestResource,
     DocumentRequestFileType,
     DocumentRequestResource,
@@ -14,6 +19,11 @@ from .errors import BadRequestError, FailedDependencyError, ForbiddenError, Inte
 
 __all__ = [
     "BadRequestError",
+    "CreateMultiResponse",
+    "CreateMultiResponseBundle",
+    "CreateMultiResponseBundleEntryItem",
+    "CreateMultiResponseBundleEntryItemRequest",
+    "CreateMultiResponseResourcesItem",
     "CreateRequestResource",
     "DocumentRequestFileType",
     "DocumentRequestResource",

phenoml/lang2fhir/client.py

@@ -5,6 +5,7 @@ import typing
 from ..core.client_wrapper import AsyncClientWrapper, SyncClientWrapper
 from ..core.request_options import RequestOptions
 from .raw_client import AsyncRawLang2FhirClient, RawLang2FhirClient
+from .types.create_multi_response import CreateMultiResponse
 from .types.create_request_resource import CreateRequestResource
 from .types.document_request_file_type import DocumentRequestFileType
 from .types.document_request_resource import DocumentRequestResource
@@ -79,6 +80,54 @@ class Lang2FhirClient:
         )
         return _response.data
 
+    def create_multi(
+        self,
+        *,
+        text: str,
+        version: typing.Optional[str] = OMIT,
+        provider: typing.Optional[str] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> CreateMultiResponse:
+        """
+        Analyzes natural language text and extracts multiple FHIR resources, returning them as a transaction Bundle.
+        Automatically detects Patient, Condition, MedicationRequest, Observation, and other resource types from the text.
+        Resources are linked with proper references (e.g., Conditions reference the Patient).
+
+        Parameters
+        ----------
+        text : str
+            Natural language text containing multiple clinical concepts to extract
+
+        version : typing.Optional[str]
+            FHIR version to use
+
+        provider : typing.Optional[str]
+            Optional FHIR provider name for provider-specific profiles
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        CreateMultiResponse
+            Successfully extracted FHIR resources
+
+        Examples
+        --------
+        from phenoml import phenoml
+
+        client = phenoml(
+            token="YOUR_TOKEN",
+        )
+        client.lang2fhir.create_multi(
+            text="John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily.",
+        )
+        """
+        _response = self._raw_client.create_multi(
+            text=text, version=version, provider=provider, request_options=request_options
+        )
+        return _response.data
+
     def search(self, *, text: str, request_options: typing.Optional[RequestOptions] = None) -> SearchResponse:
         """
         Converts natural language text into FHIR search parameters
@@ -143,9 +192,9 @@ class Lang2FhirClient:
             token="YOUR_TOKEN",
         )
         client.lang2fhir.upload_profile(
-            version="version",
-            resource="custom-patient",
-            profile="profile",
+            version="R4",
+            resource="condition-encounter-diagnosis",
+            profile="(base64 encoded JSON string of the FHIR profile)",
         )
         """
         _response = self._raw_client.upload_profile(
@@ -278,6 +327,62 @@ class AsyncLang2FhirClient:
         )
         return _response.data
 
+    async def create_multi(
+        self,
+        *,
+        text: str,
+        version: typing.Optional[str] = OMIT,
+        provider: typing.Optional[str] = OMIT,
+        request_options: typing.Optional[RequestOptions] = None,
+    ) -> CreateMultiResponse:
+        """
+        Analyzes natural language text and extracts multiple FHIR resources, returning them as a transaction Bundle.
+        Automatically detects Patient, Condition, MedicationRequest, Observation, and other resource types from the text.
+        Resources are linked with proper references (e.g., Conditions reference the Patient).
+
+        Parameters
+        ----------
+        text : str
+            Natural language text containing multiple clinical concepts to extract
+
+        version : typing.Optional[str]
+            FHIR version to use
+
+        provider : typing.Optional[str]
+            Optional FHIR provider name for provider-specific profiles
+
+        request_options : typing.Optional[RequestOptions]
+            Request-specific configuration.
+
+        Returns
+        -------
+        CreateMultiResponse
+            Successfully extracted FHIR resources
+
+        Examples
+        --------
+        import asyncio
+
+        from phenoml import Asyncphenoml
+
+        client = Asyncphenoml(
+            token="YOUR_TOKEN",
+        )
+
+
+        async def main() -> None:
+            await client.lang2fhir.create_multi(
+                text="John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily.",
+            )
+
+
+        asyncio.run(main())
+        """
+        _response = await self._raw_client.create_multi(
+            text=text, version=version, provider=provider, request_options=request_options
+        )
+        return _response.data
+
     async def search(self, *, text: str, request_options: typing.Optional[RequestOptions] = None) -> SearchResponse:
         """
         Converts natural language text into FHIR search parameters
@@ -355,9 +460,9 @@ class AsyncLang2FhirClient:
 
         async def main() -> None:
             await client.lang2fhir.upload_profile(
-                version="version",
-                resource="custom-patient",
-                profile="profile",
+                version="R4",
+                resource="condition-encounter-diagnosis",
+                profile="(base64 encoded JSON string of the FHIR profile)",
             )