nlpsandboxclient

NLP data node client that interacts with the NLP SDK client

nlpsandboxclient.client.annotate_note(host: str, note: Union[dict, nlpsandbox.model.note.Note], tool_type: str) → dict[source]

Annotate notes

Parameters

host – Data node host IP
note – Clinical note
tool_type – Type of annotator

Yields

Annotated notes

Examples

>>> example_note = {
>>>    "identifier": "note-1",
>>>    "noteType": "loinc:LP29684-5",
>>>    "patientId": "507f1f77bcf86cd799439011",
>>>    "text": "On 12/26/2020, Ms. Chloe Price met with Dr. Prescott."
>>> }
>>> annotations = annotate_note(host="0.0.0.0/api/v1",
>>>                             note=example_note,
>>>                             tool_type="date")

nlpsandboxclient.client.delete_dataset(host: str, dataset_id: str)[source]: Deletes a dataset

nlpsandboxclient.client.get_annotation(host: str, dataset_id: str, annotation_store_id: str, annotation_id: str) → nlpsandbox.model.annotation.Annotation[source]

Gets an annotation

Parameters

host – Data node host IP
dataset_id – Dataset Id
annotation_store_id – Annotation store Id
annotation_id – Annotation Id

Returns

Data node Annotation object

Examples

>>> annotation = get_annotation(
>>>     host="0.0.0.0/api/v1", dataset_id="awesome-dataset",
>>>     annotation_store_id="awesome-annotation-store",
>>>     annotation_id="awesome-annotation"
>>> )

nlpsandboxclient.client.get_annotation_store(host: str, dataset_id: str, annotation_store_id: str, create_if_missing: bool = False) → nlpsandbox.model.annotation_store.AnnotationStore[source]

Creates an annotation store

Parameters

host – Data node host IP
dataset_id – Dataset Id
annotation_store_id – Annotation store Id
create_if_missing – Creates annotation store if the resource doesn’t exist

Returns

Data node Annotation Store object

Examples

>>> annotation = create_annotation_store(
>>>     host="0.0.0.0/api/v1", dataset_id="awesome-dataset",
>>>     annotation_store_id="awesome-annotation-store"
>>> )

nlpsandboxclient.client.get_tool(host: str) → nlpsandbox.model.tool.Tool[source]

Get annotater service

Parameters: host – Annotation Service host IP
Returns: Service object
Raises: ValueError – If tool base URL isn’t redirected to tool service endpoint

Examples

>>> tool = get_tool(host="0.0.0.0/api/v1")

nlpsandboxclient.client.list_annotations(host: str, dataset_id: str, annotation_store_id: str) → Iterator[dict][source]

List annotations

Parameters

host – Data node host IP
dataset_id – Dataset Id
annotation_store_id – Annotation store Id

Yields

Data node annotation objects

Examples

>>> annotations = list_annotations(host="0.0.0.0/api/v1",
>>>                                dataset_id="awesome-dataset",
>>>                                annotation_store_id="awesome-annotation-store")

nlpsandboxclient.client.list_datasets(host: str) → List[dict][source]

Get all datasets

Parameters: host – Data node host IP
Yields: list of datasets.

Examples

>>> datasets = list_datasets(host="0.0.0.0/api/v1")
>>> list(datasets)[0]
>>> {
>>>    "name": "datasets/testing"
>>> }

nlpsandboxclient.client.list_notes(host: str, dataset_id: str, fhir_store_id: str) → List[dict][source]

Get all clinical notes for a dataset

Parameters

host – Data node host IP
dataset_id – Dataset Id
fhir_store_id – FHIR store Id

Yields

list of clinical notes.

Examples

>>> notes = get_notes(host="0.0.0.0/api/v1",
>>>                   dataset_id="awesome-dataset",
>>>                   fhir_store_id="awesome-fhir-store")
>>> list(notes)[0]
{
    "id": "noteid",
    "noteType": "",
    "patientId": "patient_id",
    "text": "Example text",
    "note_name": "dataset/awesome-dataset/fhirStores/awesome-fhirstore/fhir/Note/noteid"
}

nlpsandboxclient.client.store_annotations(host: str, dataset_id: str, annotation_store_id: str, annotations: List[dict], delete_existing_annotations: bool = True)[source]

Store submission annotated notes. Delete an annotation store if the annotation store exists, then create a new annotation store, then store the annotation.

Parameters

host – Data node host IP
dataset_id – Dataset Id
annotation_store_id – Annotation store Id
annotations – List of data node Annotations
delete_existing_annotations – To delete existing annotation store. Default is True.

nlpsandboxclient.client.store_dataset(host: str, dataset_id: str) → nlpsandbox.model.dataset.Dataset[source]: Creates a dataset

Utility functions

nlpsandboxclient.utils.camelcase_to_snakecase(value)[source]: Change camelcase to snakecase

nlpsandboxclient.utils.change_keys(obj, convert)[source]: Recursivly goes through the dictionnary obj and replaces keys with the convert function.

nlpsandboxclient.utils.check_url(url: str)[source]

Check if url is implemented

Parameters: url – The url to check
Raises: ValueError – If url is not implemented

Examples

>>> check_url(url="https://www.google.com")

nlpsandboxclient.utils.get_api_configuration(host: str)[source]

Get API configuration

Parameters: host – Tool IP
Returns: API configuration

Examples

>>> get_api_configuration(host="http://0.0.0.0:8080/api/v1")

nlpsandboxclient.utils.stdout_or_json(json_dict: dict, output: str)[source]: Write dict to json or stdout

nlpsandboxclient.utils.synapse_login(synapse_config='/github/home/.synapseConfig')[source]

Login to Synapse

Parameters: synapse_config – Path to synapse configuration file. Defaults to ~/.synapseConfig
Returns: Synapse connection