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Local Development

Check out repository:

git clone [email protected]:broadinstitute/consent-ontology.git

Build, test

cd consent-ontology
mvn clean compile
APP_NAME=consent-ontology ENV=local OUTPUT_DIR=config ../firecloud-develop/configure.rb

Tests spin up an embedded http server that run against localhost. Ensure that your test environment supports that.

Docker

Consent-Ontology is packaged into a docker image that is stored in GCR: gcr.io/broad-dsp-gcr-public/consent-ontology

# build the docker image
docker build . -t ontology

This image can then be run with the proper configuration files provided.

Render Configs

Specific to internal Broad systems:

APP_NAME=consent-ontology ENV=local OUTPUT_DIR=config ../firecloud-develop/configure.rb

Otherwise, use src/test/resources/config.yml as a template to create your own environment-specific configuration.

Spin up application:

Specific to internal Broad systems:

docker-compose -p consent-ontology -f config/docker-compose.yaml up

Or, if not using docker:

java -jar /path/to/consent-ontology.jar server /path/to/config/file

Visit local swagger page: https://local.broadinstitute.org:28443/swagger/

Debugging

Port 7777 is open in the configured docker compose. Set up a remote debug configuration pointing to local.broadinstitute.org and the defaults should be correct.

Developing with a local ElasticSearch instance:

Update the compose file to include a new section for an ES instance:

es:
  image: docker.elastic.co/elasticsearch/elasticsearch:5.5.0
  ports:
    - "9200:9200"
  volumes:
    - ../data:/usr/share/elasticsearch/data
  environment:
    transport.host: 127.0.0.1
    xpack.security.enabled: "false"
    http.host: 0.0.0.0

Add a line to the app section to link to that:

  links:
    - es:es

Finally, update the servers in consent.conf to point to this instance:

elasticSearch:
  servers:
    - es
  indexName: local-ontology

Consent will now point to a local ES instance.