usage

How to use

Input arguments

The input arguments for the central function consist of:

- variables_to_describe (dict): Dictionary of variables to describe; for categorical outliers: we assume that anything that is not in the inlier tuple is an outlier, and for numerical outliers the tuple should consist of two values, anything that is not within the range of the tuple is then considered an outlier. - variables_to_stratify (dict, optional): Dictionary of variables to stratify - organization_ids (list, optional): A list of organisation IDs that participate in the collaboration and you wish to run the algorithm on.

Examples of the variables_to_describe dictionary and the variables_to_stratify dictionary are shown below.

Python client example

To understand the information below, you should be familiar with the vantage6 framework. If you are not, please read the documentation first, especially the part about the Python client.

from vantage6.client import Client

server = 'http://localhost'
port = 5000
api_path = '/api'
private_key = None
username = 'org_1-admin'
password = 'password'

# Create connection with the vantage6 server
client = Client(server, port, api_path)
client.setup_encryption(private_key)
client.authenticate(username, password)

input_ = {
  'master': True,
  'method': 'central',
  'args': [],
  'kwargs': {
      'variables_to_describe': {'Gender': {'datatype': 'categorical',
                                           'inliers': ('M', 'F', 'X')},
                                    "Age": {"datatype": "numerical",
                                            "inliers": (15, 39)}}},
      'variables_to_stratify': None,
      'organization_ids': ['1', '2', '3']
  },
  'output_format': 'json'
}

my_task = client.task.create(
    collaboration=1,
    organizations=[1],
    name='v6-descriptive-statistics',
    description='Vantage6 algorithm that retrieves descriptive statistics ',
    image='medicaldataworks.azurecr.io/projects/strongaya/v6-descriptive-statistics',
    input=input_,
    data_format='json'
)

task_id = my_task.get('id')
results = client.wait_for_results(task_id)