Shell

Managing the database of the vantage6 server can be done by an administrator through the shell.

The preferred method of managing entities is using the API, instead of the shell interface. This because the API will perform validation of the input, whereas in the shell all inputs are accepted.

Through the shell it is possible to manage all server entities. To start the shell, use vserver shell [options].

The initialization of the shell

In the next sections the different database models that are available are explained. You can retrieve any record and edit any property of it. Don't forget to call .save() once you are done editing.

• Organizations -->db.Organization

• Users --> db.User

• Roles and Rules --> db.Role and db.Rule

• Collaborations --> db.Collaboration

• Nodes --> db.Node

• Tasks --> db.Task

• Results --> db.Result

Every db. object has a help() method which prints some info on what data is stored in it (e.g. db.Organization.help()).

Organizations

Organizations have a public key that is used for end-to-end encryption. This key is automatically created and/or uploaded by the Node the first time it's run.

To store an organization you can use the db.Organization model:

# create new organiztion
organization = db.Organization(
    name="IKNL",
    domain="iknl.nl",
    address1="Zernikestraat 29",
    address2="Eindhoven",
    zipcode="5612HZ",
    country="Netherlands"
)

# store organization in the database
organization.save()

Retrieving organizations from the database:

# get all organizations in the database
organizations = db.Organization.get()

# get organization by its unique id
organization = db.Organization.get(1)

# get organization by its name
organization = db.Organization.get_by_name("IKNL")

A lot of entities (e.g. users) at the server are connected to an organization. E.g. you can see which (computation) tasks are issued by the organization or see which collaborations it is participating in.

# retrieve organization from which we want to know more
organization = db.Organization.get_by_name("IKNL")

# get all collaborations in which the organization participates
collaborations = organization.collaborations

# get all users from the organization
users = organization.users

# get all created tasks (from all users)
tasks = organization.created_tasks

# get the results of all these tasks
results = organization.results

# get all nodes of this organization (for each collaboration
# an organization participates in, it needs a node)
nodes = organization.nodes

Roles and Rules

A user can have multiple roles and rules assigned to them. These are used to determine if the user has permission to view, edit, create or delete certain resources using the API. A role is a collection of rules.

# display all available rules
db.Rule.get()

# display rule 1
db.Rule.get(1)

# display all available roles
db.Role.get()

# display role 3
db.Role.get(3)

# show all rules that belong to role 3
db.Role.get(3).rules

# retrieve a certain rule from the DB
rule = db.Rule.get_by_("node", Scope, Operation)

# create a new role
role = db.Role(name="role-name", rules=[rule])
role.save()

# or assign the rule directly to the user
user = db.User.get_by_username("some-existing-username")
user.rules.append(rule)
user.save()

Users

Users belong to an organization. So if you have not created an organization as of yet, then you should do this first. To create a user you can use the db.User model:

# first obtain the organization to which the new user belongs
org = db.Organization.get_by_name("IKNL")

# obtain role 3 to assign to the new user
role_3 = db.Role.get(3)

# create the new users, see section Roles and Rules on how to 
# deal with permissions
new_user = db.User(
    username="root",
    password="super-secret",
    firstname="John", 
    lastname="Doe", 
    roles=[role_3],
    rules=[],
    organization=org
)

# store the user in the database
new_user.save()

You can retrieve users in the following ways:

# get all users
db.User.get()

# get user 1
db.User.get(1)

# get user by username
db.User.get_by_username("root")

# get all users from the organization IKNL
db.Organization.get_by_name("IKNL").users

To modify a user, simply adjust the properties and save the object.

user = db.User.get_by_username("some-existing-username")

# update the firstname
user.firstname = "Brandnew"

# update the password; it is automatically hashed.
user.password = "something-new"

# store the updated user in the database
user.save()

Collaborations

A collaboration consists of one or more organizations. To create a collaboration you need at least one organization in your database. To create a collaboration you can use the db.Collaboration model:

# create a second organization to collaborate with
other_organization = db.Organization(
    name="IKNL",
    domain="iknl.nl",
    address1="Zernikestraat 29",
    address2="Eindhoven",
    zipcode="5612HZ",
    country="Netherlands"
)
other_organization.save()

# get organization we have created earlier
iknl = db.Organization.get_by_name("IKNL")

# create the collaboration
collaboration = db.Collaboration(
    name="collaboration-name", 
    encrypted=False,
    organizations=[iknl, other_organization]
)

# store the collaboration in the database
collaboration.save()

Tasks, nodes and organizations are directly related to collaborations. We can obtain these by:

# obtain a collaboration which we like to inspect
collaboration = db.Collaboration.get(1)

# get all nodes
collaboration.nodes

# get all tasks issued for this collaboration
collaboration.tasks

# get all organizations
collaboration.organizations

Setting the encryption to False at the server does not mean that the nodes will send encrypted results. This is only the case if the nodes also agree on this setting.

Nodes

Before nodes can login, they need to exist in the server's database. A new node can be created as follows:

# we'll use a uuid as the API-key, but you can use anything as 
# API key
from uuid import uuid1

# nodes always belong to an organization *and* a collaboration,
# this combination needs to be unique!
iknl = db.Organization.get_by_name("IKNL")
collab = iknl.collaborations[0]

# generate and save 
api_key = str(uuid1())
print(api_key)

node = db.Node(
    name = f"IKNL Node - Collaboration {collab.name}",
    organization = iknl,
    collaboration = collab,
    api_key = api_key
)

# save the new node to the database
node.save()

API keys are hashed before stored in the database. Therefore you need to save the API key immediately. If you lose it, you can reset the API key later via the shell or via the API.

Tasks and Results

Tasks(/results) created from the shell are not picked up by nodes that are already running. The signal to notify them of a new task cannot be emitted this way.

A task is intended for one or more organizations. For each organization the task is intended for, a corresponding (initially empty) result should be created. Each task can have multiple results, for example a result from each organization.

# obtain organization from which this task is posted 
iknl = db.Organization.get_by_name("IKNL")

# obtain collaboration for which we want to create a task
collaboration = db.Collaboration.get(1)

# obtain the next run_id. Tasks sharing the same run_id
# can share the temporary volumes at the nodes. Usually this 
# run_id is assigned through the API (as the user is not allowed 
# to do so). All tasks from a master-container share the 
# same run_id
run_id = db.Task.next_run_id()

task = db.Task(
    name="some-name",
    description="some human readable description",
    image="docker-registry.org/image-name",
    collaboration=collaboration,
    run_id=run_id,
    database="default",
    initiator=iknl,
)
task.save()

# input the algorithm container (docker-registry.org/image-name) 
# expects 
input_ = {
}

import datetime

# now create a result model for each organization within the
# collaboration. This could also be a subset
for org in collaboration.organizations:
    res = db.Result(
        input=input_,
        organization=org,
        task=task,
        assigned_at=datetime.datetime.now()
    )
    res.save()

Tasks can have a child/parent relationship. Note that the run_id is for parent and child tasks the same.

# get a task to which we want to create some
# child tasks
parent_task = db.Task.get(1)

child_task = db.Task(
    name="some-name",
    description="some human readable description",
    image="docker-registry.org/image-name",
    collaboration=collaboration,
    run_id=parent_task.run_id,
    database="default",
    initiator=iknl,
    parent=parent_task
)
child_task.save()

Tasks that share a run_id have access to the same temporary folder at the node. This allows for multi-stage algorithms.

Obtaining results:

# obtain all Results
db.Result.get()

# obtain only completed results
[result for result in db.Result.get() if result.complete]

# obtain result by its unique id
db.Result.get(1)