Quickstart

Prerequisites

To access Rune’s APIs, you will need to obtain API credentials. For multi-patient analyses, we recommended using access tokens, which provide access to all the patients in your organization.

For details about creating API credentials, refer to the Stream API documentation.

Configuration

runeq uses YAML-formatted files to manage configuration settings (e.g. API credentials). The easiest way to set up this configuration is via the runeq command line tool, which is installed along with the Python library.

To get started, open a terminal and run the following command in a Python environment where runeq is installed. This command will prompt you to enter an access token ID and secret, and it will create a configuration file in the default location.

runeq configure setup

This command also provides options to get and set specific values in your config file. To see help documentation:

runeq configure --help

If you want to create or manage a configuration file manually, refer to the example config for the expected contents.

Stream API

To access the Stream API, create a V1Client, using a Config. As shown below, the configuration class uses the file that was created via the command line tool (see above).

from runeq import Config, stream

cfg = Config()
v1client = stream.V1Client(cfg)

Methods on the V1Client are used to create accessors for each type of data that can be queried using the Stream API (e.g. accelerometry, events, local field potentials, etc).

The example below initializes an Accel class, which will allow us to fetch accelerometry data:

accel = v1client.Accel(
    patient_id='992967a09cad48378f7b628aff5bdf6c',
    device_id='ABCDEF',
    start_time=1562482800,
    end_time=1563692400,
)

Accessors can be initialized with default query parameters, which will be used for all API requests.

JSON Endpoints

An accessor can be used to iterate over paginated data from the respective JSON endpoint:

for result in accel.iter_json_data():
     print(result.keys())

To override the default query parameters, use keyword arguments:

for text in accel.iter_json_data(device_id='patient-ABC,device-456'):
    pass  # do something

CSV Endpoints

An accessor can also iterate over paginated data from the respective CSV endpoint.

Here, we use the accessor to build up a pandas DataFrame, containing the complete result set.

import io
import pandas as pd

df = pd.DataFrame()
for text in accel.iter_csv_text():
    page_df = pd.read_csv(io.StringIO(text))
    df.append(page_df)

We can also iterate over each point from the CSV response. Each line from the CSV is returned as a dict:

for point in accel.points():
    print(point)

# the accessor itself is also an iterator
for point in accel:
    print(point)

To override the default query parameters, use keyword arguments:

for point in accel.points(end_time=1563692400):
    pass  # do something

for text in accel.iter_csv_text(device_id='patient-ABC,device-456'):
    pass  # do something

# etc

Note that CSV-formatted data is not supported for all resources: refer to the API documentation for details.