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Local Development

Check out repository:

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

Build, test

cd consent
mvn clean test package

Tests spin up embedded postgres and http servers that run against localhost. Ensure that your test environment supports that.

Docker

Consent docker images are stored in GCR: gcr.io/broad-dsp-gcr-public/consent

# build the docker image
docker build . -t consent

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

Render Configs

Specific to internal Broad systems:

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

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

Spin up application:

Specific to internal Broad systems:

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

Or, if not using docker:

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

Visit local swagger page: https://local.broadinstitute.org:27443/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 Elastic Search 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    
  datasetIndexName: datasetIName

Consent will now point to a local ES instance. I also suggest changing the default bucket location so uploaded ontology files do not interfere with other dev environments.