phenoml 0.0.1__py3-none-any.whl → 0.0.5__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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- phenoml/agent/__init__.py +10 -12
- phenoml/agent/client.py +172 -65
- phenoml/agent/prompts/client.py +60 -60
- phenoml/agent/prompts/raw_client.py +134 -134
- phenoml/agent/raw_client.py +236 -69
- phenoml/agent/types/__init__.py +10 -12
- phenoml/agent/types/agent_create_request.py +53 -0
- phenoml/agent/types/agent_create_request_provider.py +1 -9
- phenoml/agent/types/agent_get_chat_messages_request_order.py +5 -0
- phenoml/agent/types/agent_get_chat_messages_response.py +22 -0
- phenoml/agent/types/agent_template.py +6 -4
- phenoml/agent/types/agent_template_provider.py +1 -9
- phenoml/agent/types/chat_message_template.py +72 -0
- phenoml/agent/types/chat_session_template.py +67 -0
- phenoml/client.py +6 -0
- phenoml/core/client_wrapper.py +2 -2
- phenoml/fhir/__init__.py +36 -0
- phenoml/fhir/client.py +970 -0
- phenoml/fhir/errors/__init__.py +10 -0
- phenoml/fhir/errors/bad_request_error.py +10 -0
- phenoml/fhir/errors/internal_server_error.py +10 -0
- phenoml/fhir/errors/not_found_error.py +10 -0
- phenoml/fhir/errors/unauthorized_error.py +10 -0
- phenoml/fhir/raw_client.py +1385 -0
- phenoml/fhir/types/__init__.py +29 -0
- phenoml/{agent/types/chat_fhir_client_config.py → fhir/types/error_response.py} +11 -6
- phenoml/fhir/types/fhir_bundle.py +43 -0
- phenoml/fhir/types/fhir_bundle_entry_item.py +34 -0
- phenoml/fhir/types/fhir_bundle_entry_item_request.py +25 -0
- phenoml/fhir/types/fhir_bundle_entry_item_request_method.py +5 -0
- phenoml/fhir/types/fhir_bundle_entry_item_response.py +24 -0
- phenoml/fhir/types/fhir_patch_request_body_item.py +36 -0
- phenoml/fhir/types/fhir_patch_request_body_item_op.py +7 -0
- phenoml/fhir/types/fhir_resource.py +40 -0
- phenoml/fhir/types/fhir_resource_meta.py +28 -0
- phenoml/fhir/types/fhir_search_response.py +8 -0
- phenoml/fhir_provider/__init__.py +43 -0
- phenoml/fhir_provider/client.py +731 -0
- phenoml/fhir_provider/errors/__init__.py +11 -0
- phenoml/fhir_provider/errors/bad_request_error.py +10 -0
- phenoml/fhir_provider/errors/forbidden_error.py +10 -0
- phenoml/fhir_provider/errors/internal_server_error.py +10 -0
- phenoml/fhir_provider/errors/not_found_error.py +10 -0
- phenoml/fhir_provider/errors/unauthorized_error.py +10 -0
- phenoml/fhir_provider/raw_client.py +1445 -0
- phenoml/fhir_provider/types/__init__.py +35 -0
- phenoml/fhir_provider/types/auth_method.py +7 -0
- phenoml/fhir_provider/types/fhir_provider_auth_config.py +53 -0
- phenoml/fhir_provider/types/fhir_provider_delete_response.py +20 -0
- phenoml/fhir_provider/types/fhir_provider_list_response.py +22 -0
- phenoml/fhir_provider/types/fhir_provider_remove_auth_config_response.py +22 -0
- phenoml/fhir_provider/types/fhir_provider_response.py +22 -0
- phenoml/fhir_provider/types/fhir_provider_set_active_auth_config_response.py +22 -0
- phenoml/fhir_provider/types/fhir_provider_template.py +66 -0
- phenoml/fhir_provider/types/fhir_query_response.py +27 -0
- phenoml/fhir_provider/types/fhir_query_response_data.py +5 -0
- phenoml/fhir_provider/types/json_web_key.py +51 -0
- phenoml/fhir_provider/types/provider.py +8 -0
- phenoml/fhir_provider/types/service_account_key.py +35 -0
- phenoml/fhir_provider/types/smart_configuration.py +46 -0
- phenoml/tools/__init__.py +12 -8
- phenoml/tools/client.py +27 -60
- phenoml/tools/mcp_server/__init__.py +7 -0
- phenoml/tools/mcp_server/client.py +336 -0
- phenoml/tools/mcp_server/raw_client.py +641 -0
- phenoml/tools/mcp_server/tools/__init__.py +4 -0
- phenoml/tools/mcp_server/tools/client.py +358 -0
- phenoml/tools/mcp_server/tools/raw_client.py +656 -0
- phenoml/tools/raw_client.py +18 -67
- phenoml/tools/types/__init__.py +10 -8
- phenoml/{agent/types/agent_fhir_config.py → tools/types/mcp_server_response.py} +8 -6
- phenoml/tools/types/mcp_server_response_data.py +51 -0
- phenoml/tools/types/mcp_server_tool_call_response.py +37 -0
- phenoml/tools/types/{fhir_client_config.py → mcp_server_tool_response.py} +8 -6
- phenoml/tools/types/mcp_server_tool_response_data.py +61 -0
- {phenoml-0.0.1.dist-info → phenoml-0.0.5.dist-info}/METADATA +1 -1
- {phenoml-0.0.1.dist-info → phenoml-0.0.5.dist-info}/RECORD +79 -29
- phenoml/agent/types/agent_create_request_provider_item.py +0 -7
- phenoml/agent/types/agent_template_provider_item.py +0 -5
- phenoml/agent/types/agent_update_request_provider.py +0 -13
- phenoml/agent/types/agent_update_request_provider_item.py +0 -7
- phenoml/tools/types/cohort_request_provider.py +0 -5
- phenoml/tools/types/lang2fhir_and_create_request_provider.py +0 -7
- phenoml/tools/types/lang2fhir_and_search_request_provider.py +0 -7
- {phenoml-0.0.1.dist-info → phenoml-0.0.5.dist-info}/LICENSE +0 -0
- {phenoml-0.0.1.dist-info → phenoml-0.0.5.dist-info}/WHEEL +0 -0
phenoml/fhir/client.py
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# This file was auto-generated by Fern from our API Definition.
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import typing
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from ..core.client_wrapper import AsyncClientWrapper, SyncClientWrapper
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from ..core.request_options import RequestOptions
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from .raw_client import AsyncRawFhirClient, RawFhirClient
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from .types.fhir_bundle import FhirBundle
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from .types.fhir_bundle_entry_item import FhirBundleEntryItem
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from .types.fhir_patch_request_body_item import FhirPatchRequestBodyItem
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from .types.fhir_resource import FhirResource
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from .types.fhir_resource_meta import FhirResourceMeta
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from .types.fhir_search_response import FhirSearchResponse
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# this is used as the default value for optional parameters
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OMIT = typing.cast(typing.Any, ...)
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class FhirClient:
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def __init__(self, *, client_wrapper: SyncClientWrapper):
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self._raw_client = RawFhirClient(client_wrapper=client_wrapper)
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@property
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def with_raw_response(self) -> RawFhirClient:
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"""
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Retrieves a raw implementation of this client that returns raw responses.
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Returns
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-------
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RawFhirClient
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"""
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return self._raw_client
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def search(
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self,
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fhir_provider_id: str,
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fhir_path: str,
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*,
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query_parameters: typing.Optional[typing.Dict[str, typing.Optional[str]]] = None,
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phenoml_on_behalf_of: typing.Optional[str] = None,
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request_options: typing.Optional[RequestOptions] = None,
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) -> FhirSearchResponse:
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"""
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Retrieves FHIR resources from the specified provider. Supports both individual resource retrieval and search operations based on the FHIR path and query parameters.
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The request is proxied to the configured FHIR server with appropriate authentication headers.
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Parameters
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----------
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fhir_provider_id : str
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The ID of the FHIR provider to use. Can be either:
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- A UUID representing the provider ID
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- A provider name (legacy support - will just use the most recently updated provider with this name)
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fhir_path : str
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The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
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Examples:
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- "Patient" (for resource type operations)
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- "Patient/123" (for specific resource operations)
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- "Patient/123/_history" (for history operations)
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query_parameters : typing.Optional[typing.Dict[str, typing.Optional[str]]]
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FHIR-compliant query parameters for search operations. Supports standard FHIR search parameters including:
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- Resource-specific search parameters (e.g., name for Patient, status for Observation)
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- Common search parameters (_id, _lastUpdated, _tag, _profile, _security, _text, _content, _filter)
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- Result parameters (_count, _offset, _sort, _include, _revinclude, _summary, _elements)
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- Search prefixes for dates, numbers, quantities (eq, ne, gt, ge, lt, le, sa, eb, ap)
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phenoml_on_behalf_of : typing.Optional[str]
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Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
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request_options : typing.Optional[RequestOptions]
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Request-specific configuration.
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Returns
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-------
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FhirSearchResponse
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Successfully retrieved FHIR resource(s)
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Examples
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--------
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from phenoml import phenoml
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client = phenoml(
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token="YOUR_TOKEN",
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)
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client.fhir.search(
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fhir_provider_id="fhir_provider_id",
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fhir_path="fhir_path",
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phenoml_on_behalf_of="user@example.com",
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)
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"""
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_response = self._raw_client.search(
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fhir_provider_id,
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fhir_path,
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query_parameters=query_parameters,
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phenoml_on_behalf_of=phenoml_on_behalf_of,
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request_options=request_options,
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)
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return _response.data
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def create(
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self,
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fhir_provider_id: str,
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fhir_path: str,
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*,
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resource_type: str,
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phenoml_on_behalf_of: typing.Optional[str] = None,
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id: typing.Optional[str] = OMIT,
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meta: typing.Optional[FhirResourceMeta] = OMIT,
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request_options: typing.Optional[RequestOptions] = None,
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) -> FhirResource:
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"""
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Creates a new FHIR resource on the specified provider. The request body should contain a valid FHIR resource in JSON format.
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The request is proxied to the configured FHIR server with appropriate authentication headers.
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Parameters
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----------
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fhir_provider_id : str
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The ID of the FHIR provider to use. Can be either:
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- A UUID representing the provider ID
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- A provider name (legacy support - will just use the most recently updated provider with this name)
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fhir_path : str
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The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
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Examples:
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- "Patient" (for resource type operations)
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- "Patient/123" (for specific resource operations)
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- "Patient/123/_history" (for history operations)
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resource_type : str
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The type of FHIR resource (e.g., Patient, Observation, etc.)
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phenoml_on_behalf_of : typing.Optional[str]
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Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
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id : typing.Optional[str]
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Logical ID of the resource
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meta : typing.Optional[FhirResourceMeta]
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Metadata about the resource
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request_options : typing.Optional[RequestOptions]
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Request-specific configuration.
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Returns
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-------
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FhirResource
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Resource created successfully
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Examples
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--------
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from phenoml import phenoml
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client = phenoml(
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token="YOUR_TOKEN",
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)
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client.fhir.create(
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fhir_provider_id="fhir_provider_id",
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fhir_path="fhir_path",
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phenoml_on_behalf_of="user@example.com",
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resource_type="Patient",
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)
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"""
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_response = self._raw_client.create(
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fhir_provider_id,
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fhir_path,
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resource_type=resource_type,
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phenoml_on_behalf_of=phenoml_on_behalf_of,
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id=id,
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meta=meta,
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request_options=request_options,
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)
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return _response.data
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def upsert(
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self,
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fhir_provider_id: str,
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fhir_path: str,
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*,
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resource_type: str,
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phenoml_on_behalf_of: typing.Optional[str] = None,
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id: typing.Optional[str] = OMIT,
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meta: typing.Optional[FhirResourceMeta] = OMIT,
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request_options: typing.Optional[RequestOptions] = None,
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) -> FhirResource:
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"""
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Creates or updates a FHIR resource on the specified provider. If the resource exists, it will be updated; otherwise, it will be created.
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The request is proxied to the configured FHIR server with appropriate authentication headers.
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Parameters
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----------
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fhir_provider_id : str
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The ID of the FHIR provider to use. Can be either:
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- A UUID representing the provider ID
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- A provider name (legacy support - will just use the most recently updated provider with this name)
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fhir_path : str
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The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
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Examples:
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- "Patient" (for resource type operations)
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- "Patient/123" (for specific resource operations)
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- "Patient/123/_history" (for history operations)
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resource_type : str
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The type of FHIR resource (e.g., Patient, Observation, etc.)
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phenoml_on_behalf_of : typing.Optional[str]
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Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
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id : typing.Optional[str]
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Logical ID of the resource
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meta : typing.Optional[FhirResourceMeta]
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Metadata about the resource
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request_options : typing.Optional[RequestOptions]
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Request-specific configuration.
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Returns
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-------
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FhirResource
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Resource upserted successfully
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Examples
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--------
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from phenoml import phenoml
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client = phenoml(
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token="YOUR_TOKEN",
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)
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client.fhir.upsert(
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fhir_provider_id="fhir_provider_id",
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fhir_path="fhir_path",
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phenoml_on_behalf_of="user@example.com",
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resource_type="Patient",
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id="123",
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)
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"""
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_response = self._raw_client.upsert(
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fhir_provider_id,
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fhir_path,
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resource_type=resource_type,
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phenoml_on_behalf_of=phenoml_on_behalf_of,
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+
id=id,
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meta=meta,
|
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request_options=request_options,
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)
|
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return _response.data
|
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+
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+
def delete(
|
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self,
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fhir_provider_id: str,
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fhir_path: str,
|
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+
*,
|
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|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
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+
request_options: typing.Optional[RequestOptions] = None,
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|
+
) -> typing.Dict[str, typing.Optional[typing.Any]]:
|
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|
+
"""
|
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|
+
Deletes a FHIR resource from the specified provider.
|
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263
|
+
|
|
264
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
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265
|
+
|
|
266
|
+
Parameters
|
|
267
|
+
----------
|
|
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|
+
fhir_provider_id : str
|
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269
|
+
The ID of the FHIR provider to use. Can be either:
|
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270
|
+
- A UUID representing the provider ID
|
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271
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
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272
|
+
|
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|
+
fhir_path : str
|
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|
+
The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
|
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|
+
Examples:
|
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276
|
+
- "Patient" (for resource type operations)
|
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277
|
+
- "Patient/123" (for specific resource operations)
|
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|
+
- "Patient/123/_history" (for history operations)
|
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+
|
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280
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
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281
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
282
|
+
|
|
283
|
+
request_options : typing.Optional[RequestOptions]
|
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|
+
Request-specific configuration.
|
|
285
|
+
|
|
286
|
+
Returns
|
|
287
|
+
-------
|
|
288
|
+
typing.Dict[str, typing.Optional[typing.Any]]
|
|
289
|
+
Resource deleted successfully
|
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290
|
+
|
|
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|
+
Examples
|
|
292
|
+
--------
|
|
293
|
+
from phenoml import phenoml
|
|
294
|
+
|
|
295
|
+
client = phenoml(
|
|
296
|
+
token="YOUR_TOKEN",
|
|
297
|
+
)
|
|
298
|
+
client.fhir.delete(
|
|
299
|
+
fhir_provider_id="fhir_provider_id",
|
|
300
|
+
fhir_path="fhir_path",
|
|
301
|
+
phenoml_on_behalf_of="user@example.com",
|
|
302
|
+
)
|
|
303
|
+
"""
|
|
304
|
+
_response = self._raw_client.delete(
|
|
305
|
+
fhir_provider_id, fhir_path, phenoml_on_behalf_of=phenoml_on_behalf_of, request_options=request_options
|
|
306
|
+
)
|
|
307
|
+
return _response.data
|
|
308
|
+
|
|
309
|
+
def patch(
|
|
310
|
+
self,
|
|
311
|
+
fhir_provider_id: str,
|
|
312
|
+
fhir_path: str,
|
|
313
|
+
*,
|
|
314
|
+
request: typing.Sequence[FhirPatchRequestBodyItem],
|
|
315
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
316
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
317
|
+
) -> FhirResource:
|
|
318
|
+
"""
|
|
319
|
+
Partially updates a FHIR resource on the specified provider using JSON Patch operations as defined in RFC 6902.
|
|
320
|
+
|
|
321
|
+
The request body should contain an array of JSON Patch operations. Each operation specifies:
|
|
322
|
+
- `op`: The operation type (add, remove, replace, move, copy, test)
|
|
323
|
+
- `path`: JSON Pointer to the target location in the resource
|
|
324
|
+
- `value`: The value to use (required for add, replace, and test operations)
|
|
325
|
+
|
|
326
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
327
|
+
|
|
328
|
+
Parameters
|
|
329
|
+
----------
|
|
330
|
+
fhir_provider_id : str
|
|
331
|
+
The ID of the FHIR provider to use. Can be either:
|
|
332
|
+
- A UUID representing the provider ID
|
|
333
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
334
|
+
|
|
335
|
+
fhir_path : str
|
|
336
|
+
The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
|
|
337
|
+
Examples:
|
|
338
|
+
- "Patient" (for resource type operations)
|
|
339
|
+
- "Patient/123" (for specific resource operations)
|
|
340
|
+
- "Patient/123/_history" (for history operations)
|
|
341
|
+
|
|
342
|
+
request : typing.Sequence[FhirPatchRequestBodyItem]
|
|
343
|
+
|
|
344
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
345
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
346
|
+
|
|
347
|
+
request_options : typing.Optional[RequestOptions]
|
|
348
|
+
Request-specific configuration.
|
|
349
|
+
|
|
350
|
+
Returns
|
|
351
|
+
-------
|
|
352
|
+
FhirResource
|
|
353
|
+
Resource patched successfully
|
|
354
|
+
|
|
355
|
+
Examples
|
|
356
|
+
--------
|
|
357
|
+
from phenoml import phenoml
|
|
358
|
+
from phenoml.fhir import FhirPatchRequestBodyItem
|
|
359
|
+
|
|
360
|
+
client = phenoml(
|
|
361
|
+
token="YOUR_TOKEN",
|
|
362
|
+
)
|
|
363
|
+
client.fhir.patch(
|
|
364
|
+
fhir_provider_id="fhir_provider_id",
|
|
365
|
+
fhir_path="fhir_path",
|
|
366
|
+
phenoml_on_behalf_of="user@example.com",
|
|
367
|
+
request=[
|
|
368
|
+
FhirPatchRequestBodyItem(
|
|
369
|
+
op="replace",
|
|
370
|
+
path="/name/0/family",
|
|
371
|
+
value="NewFamilyName",
|
|
372
|
+
)
|
|
373
|
+
],
|
|
374
|
+
)
|
|
375
|
+
"""
|
|
376
|
+
_response = self._raw_client.patch(
|
|
377
|
+
fhir_provider_id,
|
|
378
|
+
fhir_path,
|
|
379
|
+
request=request,
|
|
380
|
+
phenoml_on_behalf_of=phenoml_on_behalf_of,
|
|
381
|
+
request_options=request_options,
|
|
382
|
+
)
|
|
383
|
+
return _response.data
|
|
384
|
+
|
|
385
|
+
def execute_bundle(
|
|
386
|
+
self,
|
|
387
|
+
fhir_provider_id: str,
|
|
388
|
+
*,
|
|
389
|
+
entry: typing.Sequence[FhirBundleEntryItem],
|
|
390
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
391
|
+
total: typing.Optional[int] = OMIT,
|
|
392
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
393
|
+
) -> FhirBundle:
|
|
394
|
+
"""
|
|
395
|
+
Executes a FHIR Bundle transaction or batch operation on the specified provider. This allows multiple FHIR resources to be processed in a single request.
|
|
396
|
+
|
|
397
|
+
The request body should contain a valid FHIR Bundle resource with transaction or batch type.
|
|
398
|
+
|
|
399
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
400
|
+
|
|
401
|
+
Parameters
|
|
402
|
+
----------
|
|
403
|
+
fhir_provider_id : str
|
|
404
|
+
The ID of the FHIR provider to use. Can be either:
|
|
405
|
+
- A UUID representing the provider ID
|
|
406
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
407
|
+
|
|
408
|
+
entry : typing.Sequence[FhirBundleEntryItem]
|
|
409
|
+
Array of bundle entries containing resources or operation results
|
|
410
|
+
|
|
411
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
412
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
413
|
+
|
|
414
|
+
total : typing.Optional[int]
|
|
415
|
+
Total number of resources that match the search criteria.
|
|
416
|
+
Optional field as not all FHIR servers include it (e.g., Medplum).
|
|
417
|
+
|
|
418
|
+
request_options : typing.Optional[RequestOptions]
|
|
419
|
+
Request-specific configuration.
|
|
420
|
+
|
|
421
|
+
Returns
|
|
422
|
+
-------
|
|
423
|
+
FhirBundle
|
|
424
|
+
Bundle executed successfully
|
|
425
|
+
|
|
426
|
+
Examples
|
|
427
|
+
--------
|
|
428
|
+
from phenoml import phenoml
|
|
429
|
+
from phenoml.fhir import FhirBundleEntryItem, FhirBundleEntryItemRequest
|
|
430
|
+
|
|
431
|
+
client = phenoml(
|
|
432
|
+
token="YOUR_TOKEN",
|
|
433
|
+
)
|
|
434
|
+
client.fhir.execute_bundle(
|
|
435
|
+
fhir_provider_id="fhir_provider_id",
|
|
436
|
+
phenoml_on_behalf_of="user@example.com",
|
|
437
|
+
entry=[
|
|
438
|
+
FhirBundleEntryItem(
|
|
439
|
+
resource={
|
|
440
|
+
"resourceType": "Patient",
|
|
441
|
+
"name": [{"family": "Doe", "given": ["John"]}],
|
|
442
|
+
},
|
|
443
|
+
request=FhirBundleEntryItemRequest(
|
|
444
|
+
method="POST",
|
|
445
|
+
url="Patient",
|
|
446
|
+
),
|
|
447
|
+
),
|
|
448
|
+
FhirBundleEntryItem(
|
|
449
|
+
resource={
|
|
450
|
+
"resourceType": "Observation",
|
|
451
|
+
"status": "final",
|
|
452
|
+
"subject": {"reference": "Patient/123"},
|
|
453
|
+
},
|
|
454
|
+
request=FhirBundleEntryItemRequest(
|
|
455
|
+
method="POST",
|
|
456
|
+
url="Observation",
|
|
457
|
+
),
|
|
458
|
+
),
|
|
459
|
+
],
|
|
460
|
+
)
|
|
461
|
+
"""
|
|
462
|
+
_response = self._raw_client.execute_bundle(
|
|
463
|
+
fhir_provider_id,
|
|
464
|
+
entry=entry,
|
|
465
|
+
phenoml_on_behalf_of=phenoml_on_behalf_of,
|
|
466
|
+
total=total,
|
|
467
|
+
request_options=request_options,
|
|
468
|
+
)
|
|
469
|
+
return _response.data
|
|
470
|
+
|
|
471
|
+
|
|
472
|
+
class AsyncFhirClient:
|
|
473
|
+
def __init__(self, *, client_wrapper: AsyncClientWrapper):
|
|
474
|
+
self._raw_client = AsyncRawFhirClient(client_wrapper=client_wrapper)
|
|
475
|
+
|
|
476
|
+
@property
|
|
477
|
+
def with_raw_response(self) -> AsyncRawFhirClient:
|
|
478
|
+
"""
|
|
479
|
+
Retrieves a raw implementation of this client that returns raw responses.
|
|
480
|
+
|
|
481
|
+
Returns
|
|
482
|
+
-------
|
|
483
|
+
AsyncRawFhirClient
|
|
484
|
+
"""
|
|
485
|
+
return self._raw_client
|
|
486
|
+
|
|
487
|
+
async def search(
|
|
488
|
+
self,
|
|
489
|
+
fhir_provider_id: str,
|
|
490
|
+
fhir_path: str,
|
|
491
|
+
*,
|
|
492
|
+
query_parameters: typing.Optional[typing.Dict[str, typing.Optional[str]]] = None,
|
|
493
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
494
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
495
|
+
) -> FhirSearchResponse:
|
|
496
|
+
"""
|
|
497
|
+
Retrieves FHIR resources from the specified provider. Supports both individual resource retrieval and search operations based on the FHIR path and query parameters.
|
|
498
|
+
|
|
499
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
500
|
+
|
|
501
|
+
Parameters
|
|
502
|
+
----------
|
|
503
|
+
fhir_provider_id : str
|
|
504
|
+
The ID of the FHIR provider to use. Can be either:
|
|
505
|
+
- A UUID representing the provider ID
|
|
506
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
507
|
+
|
|
508
|
+
fhir_path : str
|
|
509
|
+
The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
|
|
510
|
+
Examples:
|
|
511
|
+
- "Patient" (for resource type operations)
|
|
512
|
+
- "Patient/123" (for specific resource operations)
|
|
513
|
+
- "Patient/123/_history" (for history operations)
|
|
514
|
+
|
|
515
|
+
query_parameters : typing.Optional[typing.Dict[str, typing.Optional[str]]]
|
|
516
|
+
FHIR-compliant query parameters for search operations. Supports standard FHIR search parameters including:
|
|
517
|
+
- Resource-specific search parameters (e.g., name for Patient, status for Observation)
|
|
518
|
+
- Common search parameters (_id, _lastUpdated, _tag, _profile, _security, _text, _content, _filter)
|
|
519
|
+
- Result parameters (_count, _offset, _sort, _include, _revinclude, _summary, _elements)
|
|
520
|
+
- Search prefixes for dates, numbers, quantities (eq, ne, gt, ge, lt, le, sa, eb, ap)
|
|
521
|
+
|
|
522
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
523
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
524
|
+
|
|
525
|
+
request_options : typing.Optional[RequestOptions]
|
|
526
|
+
Request-specific configuration.
|
|
527
|
+
|
|
528
|
+
Returns
|
|
529
|
+
-------
|
|
530
|
+
FhirSearchResponse
|
|
531
|
+
Successfully retrieved FHIR resource(s)
|
|
532
|
+
|
|
533
|
+
Examples
|
|
534
|
+
--------
|
|
535
|
+
import asyncio
|
|
536
|
+
|
|
537
|
+
from phenoml import Asyncphenoml
|
|
538
|
+
|
|
539
|
+
client = Asyncphenoml(
|
|
540
|
+
token="YOUR_TOKEN",
|
|
541
|
+
)
|
|
542
|
+
|
|
543
|
+
|
|
544
|
+
async def main() -> None:
|
|
545
|
+
await client.fhir.search(
|
|
546
|
+
fhir_provider_id="fhir_provider_id",
|
|
547
|
+
fhir_path="fhir_path",
|
|
548
|
+
phenoml_on_behalf_of="user@example.com",
|
|
549
|
+
)
|
|
550
|
+
|
|
551
|
+
|
|
552
|
+
asyncio.run(main())
|
|
553
|
+
"""
|
|
554
|
+
_response = await self._raw_client.search(
|
|
555
|
+
fhir_provider_id,
|
|
556
|
+
fhir_path,
|
|
557
|
+
query_parameters=query_parameters,
|
|
558
|
+
phenoml_on_behalf_of=phenoml_on_behalf_of,
|
|
559
|
+
request_options=request_options,
|
|
560
|
+
)
|
|
561
|
+
return _response.data
|
|
562
|
+
|
|
563
|
+
async def create(
|
|
564
|
+
self,
|
|
565
|
+
fhir_provider_id: str,
|
|
566
|
+
fhir_path: str,
|
|
567
|
+
*,
|
|
568
|
+
resource_type: str,
|
|
569
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
570
|
+
id: typing.Optional[str] = OMIT,
|
|
571
|
+
meta: typing.Optional[FhirResourceMeta] = OMIT,
|
|
572
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
573
|
+
) -> FhirResource:
|
|
574
|
+
"""
|
|
575
|
+
Creates a new FHIR resource on the specified provider. The request body should contain a valid FHIR resource in JSON format.
|
|
576
|
+
|
|
577
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
578
|
+
|
|
579
|
+
Parameters
|
|
580
|
+
----------
|
|
581
|
+
fhir_provider_id : str
|
|
582
|
+
The ID of the FHIR provider to use. Can be either:
|
|
583
|
+
- A UUID representing the provider ID
|
|
584
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
585
|
+
|
|
586
|
+
fhir_path : str
|
|
587
|
+
The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
|
|
588
|
+
Examples:
|
|
589
|
+
- "Patient" (for resource type operations)
|
|
590
|
+
- "Patient/123" (for specific resource operations)
|
|
591
|
+
- "Patient/123/_history" (for history operations)
|
|
592
|
+
|
|
593
|
+
resource_type : str
|
|
594
|
+
The type of FHIR resource (e.g., Patient, Observation, etc.)
|
|
595
|
+
|
|
596
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
597
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
598
|
+
|
|
599
|
+
id : typing.Optional[str]
|
|
600
|
+
Logical ID of the resource
|
|
601
|
+
|
|
602
|
+
meta : typing.Optional[FhirResourceMeta]
|
|
603
|
+
Metadata about the resource
|
|
604
|
+
|
|
605
|
+
request_options : typing.Optional[RequestOptions]
|
|
606
|
+
Request-specific configuration.
|
|
607
|
+
|
|
608
|
+
Returns
|
|
609
|
+
-------
|
|
610
|
+
FhirResource
|
|
611
|
+
Resource created successfully
|
|
612
|
+
|
|
613
|
+
Examples
|
|
614
|
+
--------
|
|
615
|
+
import asyncio
|
|
616
|
+
|
|
617
|
+
from phenoml import Asyncphenoml
|
|
618
|
+
|
|
619
|
+
client = Asyncphenoml(
|
|
620
|
+
token="YOUR_TOKEN",
|
|
621
|
+
)
|
|
622
|
+
|
|
623
|
+
|
|
624
|
+
async def main() -> None:
|
|
625
|
+
await client.fhir.create(
|
|
626
|
+
fhir_provider_id="fhir_provider_id",
|
|
627
|
+
fhir_path="fhir_path",
|
|
628
|
+
phenoml_on_behalf_of="user@example.com",
|
|
629
|
+
resource_type="Patient",
|
|
630
|
+
)
|
|
631
|
+
|
|
632
|
+
|
|
633
|
+
asyncio.run(main())
|
|
634
|
+
"""
|
|
635
|
+
_response = await self._raw_client.create(
|
|
636
|
+
fhir_provider_id,
|
|
637
|
+
fhir_path,
|
|
638
|
+
resource_type=resource_type,
|
|
639
|
+
phenoml_on_behalf_of=phenoml_on_behalf_of,
|
|
640
|
+
id=id,
|
|
641
|
+
meta=meta,
|
|
642
|
+
request_options=request_options,
|
|
643
|
+
)
|
|
644
|
+
return _response.data
|
|
645
|
+
|
|
646
|
+
async def upsert(
|
|
647
|
+
self,
|
|
648
|
+
fhir_provider_id: str,
|
|
649
|
+
fhir_path: str,
|
|
650
|
+
*,
|
|
651
|
+
resource_type: str,
|
|
652
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
653
|
+
id: typing.Optional[str] = OMIT,
|
|
654
|
+
meta: typing.Optional[FhirResourceMeta] = OMIT,
|
|
655
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
656
|
+
) -> FhirResource:
|
|
657
|
+
"""
|
|
658
|
+
Creates or updates a FHIR resource on the specified provider. If the resource exists, it will be updated; otherwise, it will be created.
|
|
659
|
+
|
|
660
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
661
|
+
|
|
662
|
+
Parameters
|
|
663
|
+
----------
|
|
664
|
+
fhir_provider_id : str
|
|
665
|
+
The ID of the FHIR provider to use. Can be either:
|
|
666
|
+
- A UUID representing the provider ID
|
|
667
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
668
|
+
|
|
669
|
+
fhir_path : str
|
|
670
|
+
The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
|
|
671
|
+
Examples:
|
|
672
|
+
- "Patient" (for resource type operations)
|
|
673
|
+
- "Patient/123" (for specific resource operations)
|
|
674
|
+
- "Patient/123/_history" (for history operations)
|
|
675
|
+
|
|
676
|
+
resource_type : str
|
|
677
|
+
The type of FHIR resource (e.g., Patient, Observation, etc.)
|
|
678
|
+
|
|
679
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
680
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
681
|
+
|
|
682
|
+
id : typing.Optional[str]
|
|
683
|
+
Logical ID of the resource
|
|
684
|
+
|
|
685
|
+
meta : typing.Optional[FhirResourceMeta]
|
|
686
|
+
Metadata about the resource
|
|
687
|
+
|
|
688
|
+
request_options : typing.Optional[RequestOptions]
|
|
689
|
+
Request-specific configuration.
|
|
690
|
+
|
|
691
|
+
Returns
|
|
692
|
+
-------
|
|
693
|
+
FhirResource
|
|
694
|
+
Resource upserted successfully
|
|
695
|
+
|
|
696
|
+
Examples
|
|
697
|
+
--------
|
|
698
|
+
import asyncio
|
|
699
|
+
|
|
700
|
+
from phenoml import Asyncphenoml
|
|
701
|
+
|
|
702
|
+
client = Asyncphenoml(
|
|
703
|
+
token="YOUR_TOKEN",
|
|
704
|
+
)
|
|
705
|
+
|
|
706
|
+
|
|
707
|
+
async def main() -> None:
|
|
708
|
+
await client.fhir.upsert(
|
|
709
|
+
fhir_provider_id="fhir_provider_id",
|
|
710
|
+
fhir_path="fhir_path",
|
|
711
|
+
phenoml_on_behalf_of="user@example.com",
|
|
712
|
+
resource_type="Patient",
|
|
713
|
+
id="123",
|
|
714
|
+
)
|
|
715
|
+
|
|
716
|
+
|
|
717
|
+
asyncio.run(main())
|
|
718
|
+
"""
|
|
719
|
+
_response = await self._raw_client.upsert(
|
|
720
|
+
fhir_provider_id,
|
|
721
|
+
fhir_path,
|
|
722
|
+
resource_type=resource_type,
|
|
723
|
+
phenoml_on_behalf_of=phenoml_on_behalf_of,
|
|
724
|
+
id=id,
|
|
725
|
+
meta=meta,
|
|
726
|
+
request_options=request_options,
|
|
727
|
+
)
|
|
728
|
+
return _response.data
|
|
729
|
+
|
|
730
|
+
async def delete(
|
|
731
|
+
self,
|
|
732
|
+
fhir_provider_id: str,
|
|
733
|
+
fhir_path: str,
|
|
734
|
+
*,
|
|
735
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
736
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
737
|
+
) -> typing.Dict[str, typing.Optional[typing.Any]]:
|
|
738
|
+
"""
|
|
739
|
+
Deletes a FHIR resource from the specified provider.
|
|
740
|
+
|
|
741
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
742
|
+
|
|
743
|
+
Parameters
|
|
744
|
+
----------
|
|
745
|
+
fhir_provider_id : str
|
|
746
|
+
The ID of the FHIR provider to use. Can be either:
|
|
747
|
+
- A UUID representing the provider ID
|
|
748
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
749
|
+
|
|
750
|
+
fhir_path : str
|
|
751
|
+
The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
|
|
752
|
+
Examples:
|
|
753
|
+
- "Patient" (for resource type operations)
|
|
754
|
+
- "Patient/123" (for specific resource operations)
|
|
755
|
+
- "Patient/123/_history" (for history operations)
|
|
756
|
+
|
|
757
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
758
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
759
|
+
|
|
760
|
+
request_options : typing.Optional[RequestOptions]
|
|
761
|
+
Request-specific configuration.
|
|
762
|
+
|
|
763
|
+
Returns
|
|
764
|
+
-------
|
|
765
|
+
typing.Dict[str, typing.Optional[typing.Any]]
|
|
766
|
+
Resource deleted successfully
|
|
767
|
+
|
|
768
|
+
Examples
|
|
769
|
+
--------
|
|
770
|
+
import asyncio
|
|
771
|
+
|
|
772
|
+
from phenoml import Asyncphenoml
|
|
773
|
+
|
|
774
|
+
client = Asyncphenoml(
|
|
775
|
+
token="YOUR_TOKEN",
|
|
776
|
+
)
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
async def main() -> None:
|
|
780
|
+
await client.fhir.delete(
|
|
781
|
+
fhir_provider_id="fhir_provider_id",
|
|
782
|
+
fhir_path="fhir_path",
|
|
783
|
+
phenoml_on_behalf_of="user@example.com",
|
|
784
|
+
)
|
|
785
|
+
|
|
786
|
+
|
|
787
|
+
asyncio.run(main())
|
|
788
|
+
"""
|
|
789
|
+
_response = await self._raw_client.delete(
|
|
790
|
+
fhir_provider_id, fhir_path, phenoml_on_behalf_of=phenoml_on_behalf_of, request_options=request_options
|
|
791
|
+
)
|
|
792
|
+
return _response.data
|
|
793
|
+
|
|
794
|
+
async def patch(
|
|
795
|
+
self,
|
|
796
|
+
fhir_provider_id: str,
|
|
797
|
+
fhir_path: str,
|
|
798
|
+
*,
|
|
799
|
+
request: typing.Sequence[FhirPatchRequestBodyItem],
|
|
800
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
801
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
802
|
+
) -> FhirResource:
|
|
803
|
+
"""
|
|
804
|
+
Partially updates a FHIR resource on the specified provider using JSON Patch operations as defined in RFC 6902.
|
|
805
|
+
|
|
806
|
+
The request body should contain an array of JSON Patch operations. Each operation specifies:
|
|
807
|
+
- `op`: The operation type (add, remove, replace, move, copy, test)
|
|
808
|
+
- `path`: JSON Pointer to the target location in the resource
|
|
809
|
+
- `value`: The value to use (required for add, replace, and test operations)
|
|
810
|
+
|
|
811
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
812
|
+
|
|
813
|
+
Parameters
|
|
814
|
+
----------
|
|
815
|
+
fhir_provider_id : str
|
|
816
|
+
The ID of the FHIR provider to use. Can be either:
|
|
817
|
+
- A UUID representing the provider ID
|
|
818
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
819
|
+
|
|
820
|
+
fhir_path : str
|
|
821
|
+
The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
|
|
822
|
+
Examples:
|
|
823
|
+
- "Patient" (for resource type operations)
|
|
824
|
+
- "Patient/123" (for specific resource operations)
|
|
825
|
+
- "Patient/123/_history" (for history operations)
|
|
826
|
+
|
|
827
|
+
request : typing.Sequence[FhirPatchRequestBodyItem]
|
|
828
|
+
|
|
829
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
830
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
831
|
+
|
|
832
|
+
request_options : typing.Optional[RequestOptions]
|
|
833
|
+
Request-specific configuration.
|
|
834
|
+
|
|
835
|
+
Returns
|
|
836
|
+
-------
|
|
837
|
+
FhirResource
|
|
838
|
+
Resource patched successfully
|
|
839
|
+
|
|
840
|
+
Examples
|
|
841
|
+
--------
|
|
842
|
+
import asyncio
|
|
843
|
+
|
|
844
|
+
from phenoml import Asyncphenoml
|
|
845
|
+
from phenoml.fhir import FhirPatchRequestBodyItem
|
|
846
|
+
|
|
847
|
+
client = Asyncphenoml(
|
|
848
|
+
token="YOUR_TOKEN",
|
|
849
|
+
)
|
|
850
|
+
|
|
851
|
+
|
|
852
|
+
async def main() -> None:
|
|
853
|
+
await client.fhir.patch(
|
|
854
|
+
fhir_provider_id="fhir_provider_id",
|
|
855
|
+
fhir_path="fhir_path",
|
|
856
|
+
phenoml_on_behalf_of="user@example.com",
|
|
857
|
+
request=[
|
|
858
|
+
FhirPatchRequestBodyItem(
|
|
859
|
+
op="replace",
|
|
860
|
+
path="/name/0/family",
|
|
861
|
+
value="NewFamilyName",
|
|
862
|
+
)
|
|
863
|
+
],
|
|
864
|
+
)
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
asyncio.run(main())
|
|
868
|
+
"""
|
|
869
|
+
_response = await self._raw_client.patch(
|
|
870
|
+
fhir_provider_id,
|
|
871
|
+
fhir_path,
|
|
872
|
+
request=request,
|
|
873
|
+
phenoml_on_behalf_of=phenoml_on_behalf_of,
|
|
874
|
+
request_options=request_options,
|
|
875
|
+
)
|
|
876
|
+
return _response.data
|
|
877
|
+
|
|
878
|
+
async def execute_bundle(
|
|
879
|
+
self,
|
|
880
|
+
fhir_provider_id: str,
|
|
881
|
+
*,
|
|
882
|
+
entry: typing.Sequence[FhirBundleEntryItem],
|
|
883
|
+
phenoml_on_behalf_of: typing.Optional[str] = None,
|
|
884
|
+
total: typing.Optional[int] = OMIT,
|
|
885
|
+
request_options: typing.Optional[RequestOptions] = None,
|
|
886
|
+
) -> FhirBundle:
|
|
887
|
+
"""
|
|
888
|
+
Executes a FHIR Bundle transaction or batch operation on the specified provider. This allows multiple FHIR resources to be processed in a single request.
|
|
889
|
+
|
|
890
|
+
The request body should contain a valid FHIR Bundle resource with transaction or batch type.
|
|
891
|
+
|
|
892
|
+
The request is proxied to the configured FHIR server with appropriate authentication headers.
|
|
893
|
+
|
|
894
|
+
Parameters
|
|
895
|
+
----------
|
|
896
|
+
fhir_provider_id : str
|
|
897
|
+
The ID of the FHIR provider to use. Can be either:
|
|
898
|
+
- A UUID representing the provider ID
|
|
899
|
+
- A provider name (legacy support - will just use the most recently updated provider with this name)
|
|
900
|
+
|
|
901
|
+
entry : typing.Sequence[FhirBundleEntryItem]
|
|
902
|
+
Array of bundle entries containing resources or operation results
|
|
903
|
+
|
|
904
|
+
phenoml_on_behalf_of : typing.Optional[str]
|
|
905
|
+
Optional header for on-behalf-of authentication. Used when making requests on behalf of another user or entity.
|
|
906
|
+
|
|
907
|
+
total : typing.Optional[int]
|
|
908
|
+
Total number of resources that match the search criteria.
|
|
909
|
+
Optional field as not all FHIR servers include it (e.g., Medplum).
|
|
910
|
+
|
|
911
|
+
request_options : typing.Optional[RequestOptions]
|
|
912
|
+
Request-specific configuration.
|
|
913
|
+
|
|
914
|
+
Returns
|
|
915
|
+
-------
|
|
916
|
+
FhirBundle
|
|
917
|
+
Bundle executed successfully
|
|
918
|
+
|
|
919
|
+
Examples
|
|
920
|
+
--------
|
|
921
|
+
import asyncio
|
|
922
|
+
|
|
923
|
+
from phenoml import Asyncphenoml
|
|
924
|
+
from phenoml.fhir import FhirBundleEntryItem, FhirBundleEntryItemRequest
|
|
925
|
+
|
|
926
|
+
client = Asyncphenoml(
|
|
927
|
+
token="YOUR_TOKEN",
|
|
928
|
+
)
|
|
929
|
+
|
|
930
|
+
|
|
931
|
+
async def main() -> None:
|
|
932
|
+
await client.fhir.execute_bundle(
|
|
933
|
+
fhir_provider_id="fhir_provider_id",
|
|
934
|
+
phenoml_on_behalf_of="user@example.com",
|
|
935
|
+
entry=[
|
|
936
|
+
FhirBundleEntryItem(
|
|
937
|
+
resource={
|
|
938
|
+
"resourceType": "Patient",
|
|
939
|
+
"name": [{"family": "Doe", "given": ["John"]}],
|
|
940
|
+
},
|
|
941
|
+
request=FhirBundleEntryItemRequest(
|
|
942
|
+
method="POST",
|
|
943
|
+
url="Patient",
|
|
944
|
+
),
|
|
945
|
+
),
|
|
946
|
+
FhirBundleEntryItem(
|
|
947
|
+
resource={
|
|
948
|
+
"resourceType": "Observation",
|
|
949
|
+
"status": "final",
|
|
950
|
+
"subject": {"reference": "Patient/123"},
|
|
951
|
+
},
|
|
952
|
+
request=FhirBundleEntryItemRequest(
|
|
953
|
+
method="POST",
|
|
954
|
+
url="Observation",
|
|
955
|
+
),
|
|
956
|
+
),
|
|
957
|
+
],
|
|
958
|
+
)
|
|
959
|
+
|
|
960
|
+
|
|
961
|
+
asyncio.run(main())
|
|
962
|
+
"""
|
|
963
|
+
_response = await self._raw_client.execute_bundle(
|
|
964
|
+
fhir_provider_id,
|
|
965
|
+
entry=entry,
|
|
966
|
+
phenoml_on_behalf_of=phenoml_on_behalf_of,
|
|
967
|
+
total=total,
|
|
968
|
+
request_options=request_options,
|
|
969
|
+
)
|
|
970
|
+
return _response.data
|