Polaris Encounters API

The Encounters API is part of the Polaris platform (formerly DHOS). This service stores information about patient encounters (hospital stays).

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/v2/encounter	POST	Yes	Create a new encounter with the details in the request body.
/dhos/v2/encounter	GET	Yes	Get encounters matching a patient UUID or EPR encounter ID
/dhos/v1/encounter/{encounter_id}	GET	Yes	Get an encounter by its UUID
/dhos/v1/encounter/{encounter_id}	PATCH	Yes	Update an encounter by UUID using the detail provided in the request body.
/dhos/v1/encounter/{encounter_id}	DELETE	Yes	Delete data from an encounter. Only specific fields can be deleted.
/dhos/v1/encounter/{encounter_id}/children	GET	Yes	Gets the child encounter UUIDs of the encounter with the provided UUID
/dhos/v1/score_system_history/{score_system_history_id}	PATCH	Yes	Update a score system history by UUID. The score system history contains details of the different score systems used for an encounter over time.
/dhos/v1/encounter/merge	POST	Yes	Changes the patient uuid and patient record uuid for all encounters that match the given child record uuid. The old values are saved in the encounter merge history along with the message uuid. This endpoint is used when merging patients.
/dhos/v2/encounters	GET	Yes	Get encounters which have been modified after the supplied date
/dhos/v2/encounter/latest	GET	Yes	Get the latest encounter for the patient with the provided UUID
/dhos/v2/encounter/latest	POST	Yes	Retrieve latest encounters for the list of patient UUIDs provided in the request body
/dhos/v1/encounter/locations	POST	Yes	Retrieve open encounters for the list of location UUIDs provided in the request body
/dhos/v1/encounter/patients	POST	Yes	Retrieve open encounters for the list of patient UUIDs provided in the request body
/dhos/v1/encounter/locations/patient_count	POST	Yes	Retrieve count of patients for the list of location UUIDs provided in the request body

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:

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

Encounters are stored in a Postgres database.