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oclapi2

The new and improved OCL terminology service v2

Dev Setup

  1. sysctl -w vm.max_map_count=262144 #required by Elasticsearch
  2. docker compose up -d
  3. Go to http://localhost:8000/swagger/ to benefit.

Dev Setup with KeyCloak (SSO)

  1. sysctl -w vm.max_map_count=262144 #required by Elasticsearch
  2. docker compose -f docker-compose.yml -f docker-compose.sso.yml up -d
  3. Go to http://localhost:8000/swagger/ to benefit.
  4. Go to http://localhost:8080 for keyCloak.

Configuration

Authentication

OCL API supports authentication using 2 methods. One is Django Auth (integrated into API) and the other is SSO using external service supporting OpenID such as Keycloak, Active Directory, etc.

In order to setup SSO using OpenID one needs to provide the following environment variables:

OIDC_SERVER_URL=${OIDC_SERVER_URL-http://localhost:8080}
OIDC_SERVER_INTERNAL_URL=${OIDC_SERVER_INTERNAL_URL-http://host.docker.internal:8080} # only for dev env
OIDC_REALM=${OIDC_REALM-ocl}

API supports the OpenID implicit flow.

If OIDC_SERVER_URL and OIDC_REALM are not provided then the Django Auth is enabled by default.

Run Checks

(use the docker exec command in a service started with docker compose up -d)

  1. Pylint (pep8):

    docker exec -it oclapi2-api-1 pylint -j2 core

    or

    docker compose -f docker-compose.yml -f docker-compose.ci.yml run --rm api pylint -j0 core

  2. Coverage

    docker exec -it oclapi2-api-1 bash coverage.sh

    or

    docker compose -f docker-compose.yml -f docker-compose.ci.yml run --rm api bash coverage.sh

  3. Tests

    docker exec -it oclapi2-api-1 python manage.py test --keepdb -v3

    or

    docker exec -it oclapi2-api-1 python manage.py test --keepdb -v3 -- core.sources.tests.tests.SourceTest

    or

    docker compose -f docker-compose.yml -f docker-compose.ci.yml run --rm api python manage.py test --keepdb -v3

DB migrations

After modifying model you need to create migration files. Run:

docker compose run --rm api python manage.py makemigrations

Make sure to commit newly created migration files.

Indexing in ES:

  • cd oclapi2/
  • docker exec -it oclapi2-api-1 python manage.py search_index --populate -f --parallel -- for populating all indexes
  • docker exec -it oclapi2-api-1 python manage.py search_index --rebuild -f --parallel -- for rebuild (delete and create) all indexes. You can also populate/re-index specific indexes, read more

Debugging

In order to debug tests or api you can use PDB. Set a breakpoint in code with:

import pdb; pdb.set_trace()

Run tests with:

docker compose run --rm api python manage.py test core.code_systems --keepdb -v3

Run api with:

docker compose run --rm --service-ports api

Profiler

We use django-silk as our profiler

Skip to step 3 if not first time

  1. docker compose run --rm api python manage.py migrate
  2. docker compose run --rm api python manage.py collectstatic
  3. Go to http://localhost:8000/silk/

Importing FHIR resources

In order to import FHIR resources run:

docker compose run --no-deps --rm -v $(pwd)/../fhir_imports:/fhir api python tools/import.py -f /fhir -t http://api:8000/orgs/test -s 891b4b17feab99f3ff7e5b5d04ccc5da7aa96da6 -c http://api:8000/orgs/test

For help run:

docker compose run --no-deps --rm api python tools/fhir_import.py -h

Release

Every build is a candidate for release.

In order to release please trigger the release build step in our CI. Please note that the maintenance version will be automatically increased after a successful release. It is desired only, if you are releasing the latest build and should be turned off by setting the increaseMaintenanceRelease variable to false on the Run stage "Release" popup in other cases.

A deployment release will be automatically created and pushed to the staging environment.

Major/minor version increase

In order to increase major/minor version you need to set the new version in core/__init__.py. Alongside you need to login to our CI and update the next release version on a deployment plan here with the same value.

Deployment

In order to deploy please trigger the deployment here. Please use an existing deployment release.

Contributing to OCLAPI2

We welcome contributions. Please see CONTRIBUTING.md to get started!