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This is an API to the datomic database and provides data to catalyst on a per widget basis as well as information for tools like blast.
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.ebextensions fixing configuration Mar 25, 2019
scripts made it so that the dockerfile is minimal and is being created correctly Sep 19, 2016
src/rest_api made an endpoint for the version of the database that the REST API is… May 22, 2019
test Merge pull request #113 from WormBase/feature/entity-alias-uri May 22, 2017
.dockerignore made it so that the dockerfile is minimal and is being created correctly Sep 19, 2016
.gitignore finished construct started expression cluster May 19, 2017 preping for hotfix release May 20, 2019
LICENSE Initial commit Mar 16, 2014
Makefile preping for hotfix release May 20, 2019 changing name refered to in repo from datomic-to-catalyst to wormbase… Mar 22, 2019 calling create jar in jenkins bash file Apr 2, 2019
project.clj preping for hotfix release May 20, 2019
swagger3.json preping for hotfix Dec 21, 2018


  • Provide interface to datomic database to WormBase website.

Prep for deployment

  • Make sure correct WS version is specified in files
  • Make get-assembly-json
  • Change version of d-t-c in project.clj and
  • create tag (git hf release start ; docker hf release finish )


Run following commands and test each step happens correctly.

export WB_DB_URI="datomic:ddb://us-east-1/WS270/wormbase"
lein ring server-headless 8130
lein do eastwood, test
make docker-build
make run
docker ps -a
make docker-clean
git clone && checkout <tag>
eb init
make docker-tag
make docker-push-ecr
make eb-local

eb deploy

Setting environment variables

export WB_DB_URI="datomic:ddb://us-east-1/WS270/wormbase"

Starting server in development

lein ring server-headless 8130

Code quality

To run code-quality checks (linting and runs all tests):

  • Before submitting a pull request.
  • Before deploying a release.
lein code-qa

Code linting

Run lein eastwood to run the linting checks.

To have linting check for unused namespaces:

lein eastwood \
  '{:add-linter [:ununsed-namespaces] :exclude-namespace [user]}'

Running unit tests

To run tests that watch for changes in the repo:

lein test-refresh

To run all tests:

lein test

Running a local swagger JSON validator

The swagger UI displays a badge indicating whether the applications swagger.json is valid according to the specification.

The official online validator cannot work with private IP addresses, so we need to run a local swagger validator in order in development.

By default, the application will assume a local validation service is running at http://localhost:8002 (when using the lein :dev profile). This is not required, but should you not be running the service, the swagger UI page will display a broken image instead of the badge.

Clone the swagger-validator-badge repository somewhere, e.g ~/git, then run the swagger-validator service locally.

Deploying to production

Set your [AWS Credentials] [AWS Credentials]: /WormBase/wormbase-architecture/wiki/AWS-Credentials

Deploy to Clojars (to be used by other clojar projects)

lein deploy clojars

Create jar file

lein with-profile +datomic-pro,+ddb uberjar

Test deploying the jar

To see inside the jar

jar tvf ./target/<jar-name>.jar

To test:

java -jar <jar-name>.jar


Build an uberjar (with ring server support) on the local machine to avoid having to download dependencies in the container:

make clean && make docker/app.jar

Build the docker image with jar created above, and run it on the default port (3000)

make build
make run


ElasticBeanStalk is used to launch the application in the AWS plaform, using Dockcer under ECS (Elastic Container Service), using a pre-built docker image container, stored in ECR (Elastic Container Registry).

Intialize the environment (one time setup)

eb init

Testing locally

In order for the make eb-local command to work, you must have first tagged and pushed an image to ECR with:

make docker-tag
make docker-push-ecr

This assumes you have previously run make build and make run as above, and tested that the API works.

The following command will use docker login to login to the ECR repository, required in order to pull the image pushed.

Now to test the ElasticBeanStalk eb local run command, do:

make eb-local


Initial deployment:

make eb-create

For subsequent deployments, use the eb CLI directly:

eb deploy

Post-deployment tasks

  • Update project.clj to new version with -SNAPSHOT suffix e.g: "1.0-SNAPSHOT"

  • Update with new "un-released" version header and "nothing changed" stanza:

     ##[0.1.3] - (un-released)
     - nothing changed yet.
  • commit and push to develop.

Deploy to staging environment

The staging environment is relied on by and runs the latest successful build of the develop branch.

Its deployment is managed by Jenkins CI server in response to commits to the develop branch. Containers are created from the source code, and deployed on the shared dev instance.

For Jenkins CI to accomplish these tasks, it needs to be setup to with the proper dependencies. Jenkins CI server is run as the jenkins user (on the shared dev instance). In general, providing the jenkins user with a similar setup, as would be given to a human developer, would be sufficient. For example, it should be able to access docker, maven, java, lein, Datomic-pro, etc.


  • Datomic-pro needs to be manually installed or upgrade for the jenkins user. Failure to do so would break builds.
  • Jenkins might need to be restarted after an installation or other changes. This can be done with sudo /etc/init.d/jenkins restart on the shared dev instance.

For details about the Jenkins configuration, please refer to

TBD: JVM memory options.

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