Polaris Users API

The Users API is part of the Polaris platform (formerly DHOS). This service stores information about clinician users, along with their password credentials.

Maintainers

The Polaris platform was created by Sensyne Health Ltd., and has now been made open-source. As a result, some of the instructions, setup and configuration will no longer be relevant to third party contributors. For example, some of the libraries used may not be publicly available, or docker images may not be accessible externally. In addition, CICD pipelines may no longer function.

For now, Sensyne Health Ltd. and its employees are the maintainers of this repository.

Setup

These setup instructions assume you are using out-of-the-box installations of:

• pre-commit (https://pre-commit.com/)
• pyenv (https://github.com/pyenv/pyenv)
• poetry (https://python-poetry.org/)

You can run the following commands locally:

make install  # Creates a virtual environment using pyenv and installs the dependencies using poetry
make lint  # Runs linting/quality tools including black, isort and mypy
make test  # Runs unit tests

You can also run the service locally using the script run_local.sh, or in dockerized form by running:

docker build . -t <tag>
docker run <tag>

Documentation

This service originally formed part of the dhos-services-api but was split to its own services as part of ADR016

Endpoint	Method	Auth?	Description
/running	GET	No	Verifies that the service is running. Used for monitoring in kubernetes.
/version	GET	No	Get the version number, circleci build number, and git hash.
/dhos/v1/clinician	POST	Yes	Create a new clinician using the details provided in the request body.
/dhos/v1/clinician	GET	Yes	Get clinician with the provided email address.
/dhos/v1/clinician	PATCH	Yes	Update the clinician with the provided email using the details in the request body.
/dhos/v1/clinician/{clinician_id}/terms_agreement	POST	Yes	Create a new clinician terms of service agreement using the details provided in the request body.
/dhos/v1/clinician/{clinician_id}	GET	Yes	Get the clinician with the provided UUID.
/dhos/v1/clinician/{clinician_id}	PATCH	Yes	Update the clinician with the provided UUID using the details in the request body.
/dhos/v1/clinician/{clinician_id}/delete	PATCH	Yes	Remove the details in the request body from the clinician with the provided UUID. Note that this endpoint does not remove the clinician itself.
/dhos/v1/clinician/login	GET	Yes	Validate a clinician's login credentials and return a login response
/dhos/v1/clinicians	GET	Yes	Get all clinicians. Supports pagination.
/dhos/v2/clinicians	GET	Yes	Get all clinicians. Supports pagination.
/dhos/v1/clinician_list	POST	Yes	Retrieve clinicians by list of UUIDs. Response contains a map of clinician UUIDs to clinician details.
/dhos/v1/location/{location_id}/clinician	GET	Yes	Get the clinicians associated with the location with the provided UUID.
/dhos/v1/clinician/{clinician_id}/location/{location_id}/bookmark	POST	Yes	Create a bookmark between the clinician and location with the provided UUIDs.
/dhos/v1/clinician/{clinician_id}/location/{location_id}/bookmark	DELETE	Yes	Delete a bookmark between the clinician and location with the provided UUIDs.
/dhos/v1/clinician/{clinician_id}/patient/{patient_id}/bookmark	POST	Yes	Create a bookmark between the patient with the provided UUID and a clinician. Note that the clinician is determined by the JWT and not the clinician UUID in the path.
/dhos/v1/clinician/{clinician_id}/patient/{patient_id}/bookmark	DELETE	Yes	Delete a bookmark between the patient with the provided UUID and a clinician. Note that the clinician is determined by the JWT and not the clinician UUID in the path.
/dhos/v1/clinician/bulk	POST	Yes	Creates clinicians using the details provided in the request body. Intended for migration from Services API only.
/dhos/v1/roles	GET	Yes	Get a map of roles and their associated permissions

Requirements

At a minimum you require a system with Python 3.9. Tox 3.20 is required to run the unit tests, docker with docker-compose are required to run integration tests. See Development environment setup for a more detailed list of tools that should be installed.

Deployment

All development is done on a branch tagged with the relevant ticket identifier. Code may not be merged into develop unless it passes all CircleCI tests. :partly_sunny: After merging to develop tests will run again and if successful the code is built in a docker container and uploaded to our Azure container registry. It is then deployed to test environments controlled by Kubernetes.

Testing

Unit tests

🔬 Either use make or run tox directly.

tox : Running make test or tox with no arguments runs tox -e lint,default

make clean : Remove tox and pyenv virtual environments.

tox -e debug : Runs last failed unit tests only with debugger invoked on failure. Additional py.test command line arguments may given preceded by --, e.g. tox -e debug -- -k sometestname -vv

make default (or tox -e default) : Installs all dependencies, verifies that lint tools would not change the code, runs security check programs then runs unit tests with coverage. Running tox -e py39 does the same but without starting a database container.

tox -e flask : Runs flask within the tox environment. Pass arguments after --. e.g. tox -e flask -- --help for a list of commands. Use this to create database migrations.

make help : Show this help.

make lint (or tox -e lint) : Run black, isort, and mypy to clean up source files.

make openapi (or tox -e openapi) : Recreate API specification (openapi.yaml) from Flask blueprint

make pyenv : Create pyenv and install required packages (optional).

make readme (or tox -e readme) : Updates the README file with database diagram and commands. (Requires graphviz dot is installed)

make test : Test using tox

make update (or tox -e update) : Updates the poetry.lock file from pyproject.toml

Integration tests

🔩 Integration tests are located in the integration-tests sub-directory. After changing into this directory you can run the following commands:

make lint : Run black, isort, and mypy over the integration tests.

make pyenv : Creates a local Python virtual environment for the integration tests.

make test-local : Builds docker containers for the microservice and the integration tests. Other containers are pulled from Azure and Docker repositories. Note that before running this command you must be logged in to an Azure account with access to the Sensyne container repository. Use the az acr login -n sensynehealth command before running the tests or whenever your login expires.

Issue tracker

🐛 Bugs related to this microservice should be raised on Jira as PLAT-### tickets with the component set to Locations.

Database migrations

Any changes affecting the database schema should be reflected in a database migration. Simple migrations may be created automatically:

$ tox -e flask -- db migrate -m "some description"

More complex migration may be handled by creating a migration file as above and editing it by hand. Don't forget to include the reverse migration to downgrade a database.

Configuration

• DATABASE_USER, DATABASE_PASSWORD, DATABASE_NAME, DATABASE_HOST, DATABASE_PORT configure the database connection.
• LOG_LEVEL=ERROR|WARN|INFO|DEBUG sets the log level
• LOG_FORMAT=colour|plain|json configure logging format. JSON is used for the running system but the others may be more useful during development.

Database

Users are stored in a Postgres database.