oclapi2

The new and improved OCL terminology service v2

Dev Setup

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

Dev Setup with KeyCloak (SSO)

sysctl -w vm.max_map_count=262144 #required by Elasticsearch
docker-compose -f docker-compose.yml -f docker-compose.sso.yml up -d
Go to http://localhost:8000/swagger/ to benefit.
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)

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
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
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

docker-compose run --rm api python manage.py migrate
docker-compose run --rm api python manage.py collectstatic
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!

OpenConceptLab/oclapi2