1.2. Python client#

The Python client is the recommended way to interact with the vantage6 server for tasks that you want to automate. It is a Python library that facilitates communication with the vantage6 server, e.g. by encrypting and decrypting data for tasks for you.

The Python client aims to completely cover the vantage6 server communication. It can create computation tasks and collect their results, manage organizations, collaborations, users, etc. Under the hood, the Python client talks to the server API to achieve this.

1.2.1. Requirements#

You need Python to use the Python client. We recommend using Python 3.10, as the client has been tested with this version. For higher versions, it may be difficult to install the dependencies.


If you use a vantage6 version older than 3.8.0, you should use Python 3.7 instead of Python 3.10.

1.2.2. Install#

It is important to install the Python client with the same version as the vantage6 server you are talking to. Check your server version by going to https://<server_url>/version (e.g. https://cotopaxi.vantage6.ai/version or http://localhost:5000/api/version) to find its version.

Then you can install the vantage6-client with:

pip install vantage6==<version>

where you add the version you want to install. You may also leave out the version to install the most recent version.

1.2.3. Use#

First, we give an overview of the client. From the section Authentication onwards, there is example code of how to login with the client, and then create organizations, tasks etc.


The Python client contains groups of commands per resource type. For example, the group client.user has the following commands:

  • client.user.list(): list all users

  • client.user.create(username, password, ...): create a new user

  • client.user.delete(<id>): delete a user

  • client.user.get(<id>): get a user

You can see how to use these methods by using help(...) , e.g. help(client.task.create) will show you the parameters needed to create a new user:

#Create a new task
#    Parameters
#    ----------
#    collaboration : int
#        Id of the collaboration to which this task belongs
#    organizations : list
#        Organization ids (within the collaboration) which need
#        to execute this task
#    name : str
#        Human readable name
#    image : str
#        Docker image name which contains the algorithm
#    description : str
#        Human readable description
#    input : dict
#        Algorithm input
#    database: str, optional
#        Name of the database to use. This should match the key
#        in the node configuration files. If not specified the
#        default database will be tried.
#    Returns
#    -------
#    dict
#        Containing the task information

The following groups (related to the Entities) of methods are available. They usually have list(), create(), delete() and get() methods attached - except where they are not relevant (for example, a rule that gives a certain permission cannot be deleted).

  • client.user

  • client.organization

  • client.rule

  • client.role

  • client.collaboration

  • client.task

  • client.run

  • client.result

  • client.node

Finally, the class client.util contains some utility functions, for example to check if the server is up and running or to change your own password.


This section and the following sections introduce some minimal examples for administrative tasks that you can perform with our Python client. We start by authenticating.

To authenticate, we create a config file to store our login information. We do this so we do not have to define the server_url, server_port and so on every time we want to use the client. Moreover, it enables us to separate the sensitive information (login details, organization key) that you do not want to make publicly available, from other parts of the code you might write later (e.g. on submitting particular tasks) that you might want to share publicly.

# config.py

server_url = "https://MY VANTAGE6 SERVER" # e.g. https://cotopaxi.vantage6.ai or
                                          # http://localhost for a local dev server
server_port = 443 # This is specified when you first created the server
server_api = "" # This is specified when you first created the server

username = "MY USERNAME"
password = "MY PASSWORD"

organization_key = "FILEPATH TO MY PRIVATE KEY" # This can be empty if you do not want to set up encryption

Note that the organization_key should be a filepath that points to the private key that was generated when the organization to which your login belongs was first created (see Creating an organization).

Then, we connect to the vantage 6 server by initializing a Client object, and authenticating

from vantage6.client import UserClient as Client

# Note: we assume here the config.py you just created is in the current directory.
# If it is not, then you need to make sure it can be found on your PYTHONPATH
import config

# Initialize the client object, and run the authentication
client = Client(config.server_url, config.server_port, config.server_api,
client.authenticate(config.username, config.password)

# Optional: setup the encryption, if you have an organization_key

Creating an organization#

After you have authenticated, you can start generating resources. The following also assumes that you have a login on the Vantage6 server that has the permissions to create a new organization. Regular end-users typically do not have these permissions (typically only administrators do); they may skip this part.

The first (optional, but recommended) step is to create an RSA keypair. A keypair, consisting of a private and a public key, can be used to encrypt data transfers. Users from the organization you are about to create will only be able to use encryption if such a keypair has been set up and if they have access to the private key.

from vantage6.common import warning, error, info, debug, bytes_to_base64s
from vantage6.client.encryption import RSACryptor
from pathlib import Path

# Generated a new private key
# Note that the file below doesn't exist yet: you will create it
private_key_filepath = r'/path/to/private/key'
private_key = RSACryptor.create_new_rsa_key(Path(private_key_filepath))

# Generate the public key based on the private one
public_key_bytes = RSACryptor.create_public_key_bytes(private_key)
public_key = bytes_to_base64s(public_key_bytes)

Now, we can create an organization

    name = 'The_Shire',
    address1 = '501 Buckland Road',
    address2 = 'Matamata',
    zipcode = '3472',
    country = 'New Zealand',
    domain = 'the_shire.org',
    public_key = public_key   # use None if you haven't set up encryption

Users can now be created for this organization. Any users that are created and who have access to the private key we generated above can now use encryption by running

# or, if you don't use encryption

after they authenticate.

Creating a collaboration#

Here, we assume that you have a Python session with an authenticated Client object, as created in Authentication. We also assume that you have a login on the Vantage6 server that has the permissions to create a new collaboration (regular end-users typically do not have these permissions, this is typically only for administrators).

A collaboration is an association of multiple organizations that want to run analyses together. First, you will need to find the organization id’s of the organizations you want to be part of the collaboration.

client.organization.list(fields=['id', 'name'])

Once you know the id’s of the organizations you want in the collaboration (e.g. 1 and 2), you can create the collaboration:

collaboration_name = "fictional_collab"
organization_ids = [1,2] # the id's of the respective organizations
client.collaboration.create(name = collaboration_name,
                            organizations = organization_ids,
                            encrypted = True)

Note that a collaboration can require participating organizations to use encryption, by passing the encrypted = True argument (as we did above) when creating the collaboration. It is recommended to do so, but requires that a keypair was created when Creating an organization and that each user of that organization has access to the private key so that they can run the client.setup_encryption(...) command after Authentication.

Registering a node#

Here, we again assume that you have a Python session with an authenticated Client object, as created in Authentication, and that you have a login that has the permissions to create a new node (regular end-users typically do not have these permissions, this is typically only for administrators).

A node is associated with both a collaboration and an organization (see Entities). You will need to find the collaboration and organization id’s for the node you want to register:

client.organization.list(fields=['id', 'name'])
client.collaboration.list(fields=['id', 'name'])

Then, we register a node with the desired organization and collaboration. In this example, we create a node for the organization with id 1 and collaboration with id 1.

# A node is associated with both a collaboration and an organization
organization_id = 1
collaboration_id = 1
api_key = client.node.create(collaboration = collaboration_id, organization = organization_id)
print(f"Registered a node for collaboration with id {collaboration_id}, organization with id {organization_id}. The API key that was generated for this node was {api_key}")

Remember to save the api_key that is returned here, since you will need it when you Configure the node.

Creating a task#


Here we assume that

  • you have a Python session with an authenticated Client object, as created in Authentication.

  • you already have the algorithm you want to run available as a container in a docker registry (see here for more details on developing your own algorithm)

  • the nodes are configured to look at the right database

In this manual, we’ll use the averaging algorithm from harbor2.vantage6.ai/demo/average, so the second requirement is met. We’ll assume the nodes in your collaboration have been configured to look as something like:

   - label: default
     uri: /path/to/my/example.csv
     type: csv
   - label: my_other_database
     uri: /path/to/my/example2.csv
     type: excel

The third requirement is met when all nodes have the same labels in their configuration. As an end-user running the algorithm, you’ll need to align with the node owner about which database name is used for the database you are interested in. For more details, see how to configure your node.

Determining which collaboration / organizations to create a task for

First, you’ll want to determine which collaboration to submit this task to, and which organizations from this collaboration you want to be involved in the analysis

>>> client.collaboration.list(fields=['id', 'name', 'organizations'])
 {'id': 1, 'name': 'example_collab1',
 'organizations': [
     {'id': 2, 'link': '/api/organization/2', 'methods': ['GET', 'PATCH']},
     {'id': 3, 'link': '/api/organization/3', 'methods': ['GET', 'PATCH']},
     {'id': 4, 'link': '/api/organization/4', 'methods': ['GET', 'PATCH']}

In this example, we see that the collaboration called example_collab1 has three organizations associated with it, of which the organization id’s are 2, 3 and 4. To figure out the names of these organizations, we run:

>>> client.organization.list(fields=['id', 'name'])
[{'id': 1, 'name': 'root'}, {'id': 2, 'name': 'example_org1'},
 {'id': 3, 'name': 'example_org2'}, {'id': 4, 'name': 'example_org3'}]

i.e. this collaboration consists of the organizations example_org1 (with id 2), example_org2 (with id 3) and example_org3 (with id 4).

Creating a task that runs the central algorithm

Now, we have two options: create a task that will run the central part of an algorithm (which runs on one node and may spawns subtasks on other nodes), or create a task that will (only) run the partial methods (which are run on each node). Typically, the partial methods only run the node local analysis (e.g. compute the averages per node), whereas the central methods performs aggregation of those results as well (e.g. starts the partial analyses and then computes the overall average). First, let us create a task that runs the central part of the harbor2.vantage6.ai/demo/average algorithm:

input_ = {
    'method': 'central_average',
    'kwargs': {'column_name': 'age'}

average_task = client.task.create(
      {'label': 'default'}

Note that the kwargs we specified in the input_ are specific to this algorithm: this algorithm expects an argument column_name to be defined, and will compute the average over the column with that name. Furthermore, note that here we created a task for collaboration with id 1 (i.e. our example_collab1) and the organizations with id 2 and 3 (i.e. example_org1 and example_org2). I.e. the algorithm need not necessarily be run on all the organizations involved in the collaboration.

Finally, note that you should provide any databases that you want to use via the databases argument. In the example above, we use the default database; using the my_other_database database can be done by simply specifying that label in the dictionary. If you have a SQL, SPARQL or OMOP database, you should also provide a query argument, e.g.

   {'label': 'default', 'query': 'SELECT * FROM my_table'}

Similarly, you can define a sheet_name for Excel databases if you want to read data from a specific worksheet. Check help(client.task.create) for more information.

Creating a task that runs the partial algorithm

You might be interested to know output of the partial algorithm (in this example: the averages for the ‘age’ column for each node). In that case, you can run only the partial algorithm, omitting the aggregation that the central part of the algorithm will normally do:

input_ = {
    'method': 'partial_average',
    'kwargs': {'column_name': 'age'},

average_task = client.task.create(collaboration=1,

Inspecting the results

Of course, it will take a little while to run your algorithm. You can use the following code snippet to run a loop that checks the server every 3 seconds to see if the task has been completed:

print("Waiting for results")
task_id = average_task['id']
result = client.wait_for_results(task_id)

You can also check the status of the task using:

task_info = client.task.get(task_id, include_results=True)

and then retrieve the results

result_info = client.result.from_task(task_id=task_id)

The number of results may be different depending on what you run, but for the central average algorithm in this example, the results would be:

>>> result_info
[{'average': 53.25}]

while for the partial algorithms, dispatched to two nodes, the results would be:

>>> result_info
[{'sum': 253, 'count': 4}, {'sum': 173, 'count': 4}]