Compare Backend

This is the backend/middleware component of the Compare application.

Getting started

Prerequisites

In order to build the application, you need Docker and Docker Compose. For development and testing, you also need Apache Maven 3 and JDK 1.8.

How to set environment variables

• Windows
• Mac
• Linux:
  • Open /etc/environment in a text editor
  • For each variable, add a line of the form export VARIABLE_NAME=value
  • Run source /etc/environment in a terminal
  • The variables should now be set for that terminal session. They will be set globally whenever the system reboots.

Installing for local development

First, set the following environment variables:

MONGODB_INITDB_ROOT_USERNAME: username
MONGODB_INITDB_ROOT_PASSWORD: password
MONGODB_INITDB_DATABASE: compare
MONGODB_PORT: 27017
ANALYSIS_PROTOCOL: http
ANALYSIS_URL: analysis
COMPARE_CYTOMINE_URL: https://core.example.com
COMPARE_ADMIN_PUB_KEY: public key
COMPARE_ADMIN_PRIV_KEY: private key

The variable COMPARE_CYTOMINE_URL should contain the URL of the Cytomine instance hosting the images for comparison. The variables COMPARE_ADMIN_{PUB, PRIV}_KEY should contain a key pair that can be used to connect to this instance.

Secondly, copy the contents of .analysis.env.sample into a file called .analysis_dev.env.

Finally, run the command docker-compose -f docker-compose.dev.yml up --build -d. A development container will become available at http://localhost:9292.

Testing

Preparing to run the integration tests

Before you can run the integration tests, you have to set some environment variables:

COMPARE_TEST_MONGODB_HOST: localhost
COMPARE_TEST_MONGODB_PORT: 27018
COMPARE_TEST_MONGODB_ROOT_USERNAME: admin
COMPARE_TEST_MONGODB_ROOT_PASSWORD: password123
COMPARE_TEST_MONGODB_DATABASE: compare_test
COMPARE_TEST_TOMCAT_PROTOCOL: http
COMPARE_TEST_TOMCAT_HOST: localhost
COMPARE_TEST_TOMCAT_PORT: 8081

In addition, you need to copy the contents of the file .analysis.env.sample into a file with the name .analysis_test.env.

Running the tests

The integration tests will only work if the application is already running. You can start it in a test container with the command ./integration_test_setup.sh, and stop it with the command ./integration_test_teardown.sh. You may need to add the prefix sudo -E to these commands.

To run the unit tests and integration tests:

mvn verify

To run only the unit tests:

mvn test

To run only the integration tests:

mvn -Dskip.unit.tests=true verify

To run the style tests:

mvn checkstyle:check

Deployment

We recommend using the infrastructure repository for deploying to production.

Documentation

The API is described in API.md.

Contributing

See CONTRIBUTING.md.

License

See LICENSE.