Quickstart

Prerequisites

API Credentials

To access Rune’s APIs, you will need to obtain API credentials. For multi-patient analyses, we recommended using user access tokens.

Note

If you belong to multiple organizations, note that only one organization is “active” at a time. You can only access resources that belong to your active organization. This impacts both what is returned by the SDK and what you see in the Rune web portal.

You can change your active organization through code (see Set Active Org) or in the Rune web portal (click on the profile icon, in the top right corner).

To create a new access token:

  1. Log in to the Rune web portal

  2. Click on the profile icon, in the top right corner.

  3. Click on User Settings.

  4. On the left sidebar, click on Access Tokens.

  5. Click CREATE ACCESS TOKEN.

  6. Copy the token ID and secret before closing the page. The secret will never be shown again.

See Configuration Setup for details about how to use these credentials with this library.

It is highly recommended that you rotate your access tokens every 3-6 months, by creating a new token and deactivating the old one. Store your access tokens securely, and do not share them.

Configuration Setup

runeq uses a YAML-formatted file 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.

Once a configuration file exists, you won’t need to repeat this step (unless you’re rotating your access token, getting set up on a different computer, etc).

Initialization

To get started with the library, use initialize. This loads credentials from your configuration file (see Configuration Setup).

from runeq import initialize

initialize()

To see information about your authenticated user:

from runeq.resources.user import get_current_user

my_user = get_current_user()
print(my_user)
print('Active Org:', my_user.active_org_name)

Usage

Set Active Org

To get metadata about all the organizations that you belong to:

from runeq.resources.org import get_orgs

all_orgs = get_orgs()
for org in all_orgs:
    print(org)

You can set your active organization using an org ID:

from runeq.resources.org import set_active_org

org_id = "aa0c21f97d6a0593b0a247c68f015d68b787655e"
active_org = set_active_org(org_id)
print('Active Org:', active_org.name)

Explore Metadata

After initializing the library, you can fetch metadata about various resources.

For example, you can fetch metadata about all the patients in your active org:

from runeq.resources.patient import get_all_patients

patients = get_all_patients()

for patient in patients:
    print(patient)
    for device in patient.devices:
        print(' ', device)

    print('')

get_all_patients returns a PatientSet. This object can be serialized as a list of dictionaries, e.g. to save the metadata to a file:

import json

with open('patients.json', 'w') as f:
    json.dump(patients.to_list(), f, indent=4)

You can also convert a PatientSet to a collection of devices (a DeviceSet). This may be more convenient for a columnar data format, like a pandas DataFrame.

import pandas as pd

devices = patients.devices
devices_df = pd.DataFrame(devices.to_list())

Similarly to fetching information about patients, you can fetch information about projects, and metadata related to the patients within projects (and cohorts).

You can find information about a single project:

from runeq.resources.project import get_project, get_project_patients, get_cohort_patients

# Fetch basic metadata about a project (title, description, cohorts)
project = get_project(project_id="example_project_id")
print(project.to_dict())

# Fetch metadata for the patients within a project
project_patients = get_project_patients(project_id="example_project_id")
for project_patient in project_patients:
    print(project_patient)

# You can create a dataframe of the project patient metadata
project_patient_metadata_df = project_patients.to_dataframe()

# You can also fetch the list of patients in a cohort, using a cohort ID.
cohort_patients = get_cohort_patients(cohort_id="example_cohort_id")
cohort_patient_metadata_df = cohort_patients.to_dataframe()

Fetch Timeseries Data

Use get_patient_stream_metadata to get a StreamMetadataSet with details about a particular patient’s data. If you’re interested in a more specific set of streams, the function accepts additional filters.

from runeq.resources.stream_metadata import get_patient_stream_metadata

patient_id = "c4bd060df1454aa0adc978985512c6e9"
patient_streams = get_patient_stream_metadata(patient_id)
print(f'Found {len(patient_streams)} streams')

Once you have a StreamMetadataSet, you can use the filter operation to get a more specific subset of streams:

# Filter for data collected from a particular device
device_id = "eb#8c31"
device_streams = patient_streams.filter(device_id=device_id)

# Filter by broad category
neural_streams = patient_streams.filter(category="neural")

# Specify multiple arguments to find streams that match
# all criteria
neural_device_streams = patient_streams.filter(
    category="neural",
    device_id=device_id,
)

# Use a custom filter function
import time

def in_last_two_weeks(stream) -> bool:
    """Return True if stream has data in the last two weeks"""
    two_weeks_ago = time.time() - 14*24*60*60
    return stream.max_time > two_weeks_ago

recent_vitals_streams = patient_streams.filter(
    category="vitals",
    filter_function=in_last_two_weeks
)

You can also combine multiple StreamMetadataSet s, using update:

from runeq.resources.stream_metadata import StreamMetadataSet

lfp_power_streams = patient_streams.filter(
    category="neural",
    measurement="lfp_trend_log_power",
)
tremor_streams = patient_streams.filter(
    category="symptom",
    measurement="tremor",
    stream_type_id="duration"
)

lfp_and_tremor_streams = StreamMetadataSet()
lfp_and_tremor_streams.update(lfp_power_streams)
lfp_and_tremor_streams.update(tremor_streams)

Using a StreamMetadataSet, you can fetch the availability of all or any of the streams:

availability_df = lfp_and_tremor_streams.get_batch_availability_dataframe(
    start_time=1662000000,
    end_time=1663123000,
    resolution=3600,
    batch_operation="any",
)

Note

The API for “batch availability” has a limit on the number of streams that it can process at a time. If you’re running the example code with a patient who has multiple devices, the snippet above may exceed the API limit. Try limiting the number of streams in the set using a custom filter function, to select for a few of those device IDs.

When you’re ready to fetch data, you can gather all the raw stream data into a pandas dataframe:

stream_df = lfp_and_tremor_streams.get_stream_dataframe(
    start_time=1662499000,
    end_time=1663123000,
)

You can also work directly with responses from the V2 Stream API. See stream and StreamMetadata for details.

Fetch StrivePD Events

The StrivePD app allows users to log events related to their health and well-being. Events fall into many categories, including:

  • Activities (manually logged or ingested from HealthKit)

  • Medication and supplement logs

  • Symptom logs

  • Wellbeing logs

  • Free-text notes

To query StrivePD events, you will need a patient ID and a time range:

from runeq.resources.event import get_patient_events

event_set = get_patient_events(
    patient_id="TODO",
    start_time=1662000000,
    end_time=1663123000,
)

# For easy data manipulation, convert the EventSet to a pandas DataFrame
events_df = event_set.to_dataframe()

The event module also provides helper functions to query events of a specific type. For example, to fetch activity events:

from runeq.resources.event import get_patient_activity_events

activity_event_set = get_patient_activity_events(
    patient_id="TODO",
    start_time=1662000000,
    end_time=1663123000,
)

activity_events_df = activity_event_set.to_dataframe()
# Similarly, you can fetch medication events, symptom events, wellbeing events, etc.

Note

Many StrivePD events are also queryable as streams (with the algorithm ingest-rune-events). The stream representation of the data is less reliable and may not reflect the latest state of user data. Whenever possible, we recommend querying StrivePD events with the functionality from the event module.