Informatics Matters Squonk2 Python Client

A Python 3 package that provides simplified access to key parts of the Informatics Matters Squonk2 service, consisting of the Authentication, and Data Manager and Account Server REST interfaces. The functions provide access to some of the key API methods, implemented initially to support execution of Jobs from a Fragalysis stack backend.

Note

Odd numbered major versions of the client are used for the synchronous API and even-numbered major versions are used for the asynchronous API. Version 1.x.x of the client can only be used against the Data Manager version 1. Version 3.x.x must be used for Data Manager version 2 and later.

Simplified Authentication

The following Squonk2 Authentication functions are available: -

• Auth.get_access_token()

Simplified Data Manager API

The following Squonk2 Data Manager API functions are available: -

• DmApi.set_api_url()
• DmApi.get_api_url()
• DmApi.ping()
• DmApi.add_project_editor()
• DmApi.add_project_observer()
• DmApi.create_project()
• DmApi.delete_instance()
• DmApi.delete_instance_token()
• DmApi.delete_project()
• DmApi.delete_unmanaged_project_files()
• DmApi.dry_run_job_instance()
• DmApi.get_account_server_namespace()
• DmApi.get_account_server_registration()
• DmApi.get_available_instances()
• DmApi.get_available_datasets()
• DmApi.get_available_jobs()
• DmApi.get_available_projects()
• DmApi.get_available_tasks()
• DmApi.get_job()
• DmApi.get_job_exchange_rates()
• DmApi.get_job_by_version()
• DmApi.get_instance()
• DmApi.get_project()
• DmApi.get_project_instances()
• DmApi.get_service_errors()
• DmApi.get_task()
• DmApi.get_tasks()
• DmApi.get_unmanaged_project_file()
• DmApi.get_unmanaged_project_file_with_token()
• DmApi.get_version()
• DmApi.list_project_files()
• DmApi.put_unmanaged_project_files()
• DmApi.put_job_manifest()
• DmApi.remove_project_editor()
• DmApi.remove_project_observer()
• DmApi.set_admin_state()
• DmApi.set_job_exchange_rates()
• DmApi.start_job_instance()

A dataclass is used as the return value for many of the methods: -

• DmApiRv

It contains a boolean success field and a dictionary msg field. The msg typically contains the underlying REST API response content (rendered as a Python dictionary), or an error message if the call failed.

Simplified Account Server API

The following Squonk2 Account Server API functions are available: -

• AsApi.set_api_url()
• AsApi.get_api_url()
• AsApi.ping()
• AsApi.create_product()
• AsApi.create_unit()
• AsApi.create_organisation()
• AsApi.delete_product()
• AsApi.delete_unit()
• AsApi.get_available_assets()
• AsApi.get_available_units()
• AsApi.get_available_products()
• AsApi.get_merchants()
• AsApi.get_organisation()
• AsApi.get_product()
• AsApi.get_products_for_unit()
• AsApi.get_products_for_organisation()
• AsApi.get_product_charges()
• AsApi.get_organisations()
• AsApi.get_unit()
• AsApi.get_units()
• AsApi.get_version()

A dataclass is used as the return value for many of the methods: -

• AsApiRv

It contains a boolean success field and a dictionary msg field. The msg typically contains the underlying REST API response content (rendered as a Python dictionary), or an error message if the call failed.

Simplified UI API

The following Squonk2 UI API functions are available: -

• UiApi.set_api_url()
• UiApi.get_version()

A namedtuple is used as the return value for many of the methods: -

• UiApiRv

It contains a boolean success field and a dictionary msg field. The msg typically contains the underlying REST API response content (rendered as a Python dictionary), or an error message if the call failed.

Examples

The package ships with some API examples that might be useful for your own work. They are located in the package examples module, where the following imports should be available: -

• from squonk2.examples.data_manager import job_chain

Debugging the API requests

For development purposes you can expose detailed debug information relating to the underlying API requests by setting the environment variable SQUONK2_API_DEBUG_REQUESTS:

export SQUONK2_API_DEBUG_REQUESTS=yes

This will enable detailed debug of both the DM and AS API calls.

Installation

The Squonk2 package is published on PyPI and can be installed from there:

pip install im-squonk2-client

Environment module

The API contains a convenient Environment module that allows you to keep your environment variables in a file so that you don't need to declare them in the shell. The default location of the file is ~/.squonk2/environments. If you have multiple installations this allows you to keep all your environment settings together in one file.

You can use an alternative file by setting SQUONK2_ENVIRONMENTS_FILE, e.g. export SQUONK2_ENVIRONMENTS_FILE=~/my-env'

---

# An example Squeck environments file.
#
# It provides all the connection details for one or more Squonk2 environments.
# It is expected to be found in the user's home directory
# as '~/.squonk2/environments' or the user can 'point' to it by setting
# 'SQUONK2_ENVIRONMENTS_FILE', e.g. 'export SQUONK2_ENVIRONMENTS_FILE=~/my-env'

# The 'environments' block defines one or more environments.
# Each has a name. Here we define an environment called 'site-a'
# but environments can be called anything YAML accepts as a key,
# although it would aid consistency if you restrict your names to letters
# and hyphens.
environments:
  site-a:
    # The hostname of the keycloak server, without a 'http' prefix
    # and without a '/auth' suffix.
    keycloak-hostname: example.com
    # The realm name used for the Squonk2 environment.
    keycloak-realm: squonk2
    # The Keycloak client IDs of the Account Server and Data Manager.
    # The Account Server client ID is optional.
    keycloak-as-client-id: account-server-api
    keycloak-dm-client-id: data-manager-api
    # The hostnames of the Account Server and Data Manager APIs,
    # without a 'http' prefix and without an 'api' suffix.
    # If you have not provided an Account Server client ID its
    # hostname value is not required.
    as-hostname: as.example.com
    dm-hostname: dm.example.com
    # The username and password of an admin user that has access
    # to the Account Server and Data Manager.
    # The user *MUST* have admin rights.
    admin-user: dlister
    admin-password: blob1234

# The final part of the file is a 'default' property,
# which Squeck (Squonk Deck) uses to select the an environment from the block above
# when all else fails. It's simply the name of one of the environment
# declarations above.
default: site-a

To avoid placing admin-user and admin-password values into the Environment file you can provide them through environment variables that are scoped to the environment name. For example, in the above you could omit them both and provide them as values using the following variables: -

• SQUONK2_ENVIRONMENT_SITE_A_ADMIN_USER
• SQUONK2_ENVIRONMENT_SITE_A_ADMIN_PASSWORD

Using the Environment

from squonk2.environment import Environment

_ = Environment.load()
environment: Environment = Environment('site-a')
# Get the AS API for 'local'
# The hostname is augmented so you will get (for the above example)
# the value 'https://as.example.com/account-server-api'
as_api: str = environment.as_api()

Documentation

Documentation is available in the squonk2-python-client project on Read the Docs

Get in touch

• Report bugs, suggest features or view the source code on GitHub.