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Cytomine Core

Install

See our Cytomine-bootstrap project to install it with Docker. A branch spring-core has the modification to install the core in its spring version (v4).

WARNING: The current beta version does not support already existing dataset created from previous version. You can only create Cytomine instance with an empty dataset. This will be supported in the final v4.0.0+.

Run tests

Automated tests require:

  • A postgresql with postgis
  • A mongodb
  • A rabbitMQ

You can simply run the docker-compose configuration from scripts/docker-compose.yml in order to have all these dependencies up and running with the right configuration.

docker-compose -f scripts/docker-compose-test.yml up -d

Tests can be executed with Gradle:

./gradlew :test

Or via your favorite IDE (right click on /src/test/java and choose Run Tests in cytomine-core)

After tests, you can shutdown the configuration :

docker-compose -f scripts/docker-compose-test.yml down -v

Run as dev

Execute the main class src/main/java/be/cytomine/CytomineCoreApplication.java

Build an executable

./gradlew bootJar produce a auto-executable jar under build/libs/cytomine.jar

Run it using:

java -jar /app/cytomine.jar

Override configuration

Default application configuration values are located in src/main/resources/application.yml. You can override them by creating a application.yml or .properties in the application root directory.

Jenkins

A Jenkins file is provided.

  1. Retrieve source code from repository
  2. Compute the current version based on the current commit tag (if a tag has been defined)
    • git tag -a "v$x.$y.$z" (e.g. v1.2.3) in order to defne an official release
    • git tag -a "v$x.$y.$z-beta.$n" (e.g. v1.2.3-beta.5) in order to defne an beta release
    • Otherwise a name will be generated from the branche name and the datetime
  3. Download core dependencies
  4. Run postgresql, mongodb and rabbitmq thanks to docker-compose
  5. Run tests
  6. Publish tests results reports on Jenkins
  7. Publish tests coverage reports on Jenkins
  8. Shutdown postgresql, mongodb and rabbitmq configurations.
  9. Build and publish a jar
  10. Build and publish a docker image.

Upgrade from old version Cytomine dataset

The upgrade only works with a dataset from at least core 3.2.0.

We will provide soon a automated way to upgrade databases

Postgresql database: Regarding Postgresql, nothing to be done. Liquibase should apply changes during the first run.

MongoDB database: As we are moving from MongoDB v2 to v4, the current migration process needs:

  • extract the current mongodb database .json / .bson files
  • import them using ./scripts/migration/import_mongo.sh into the new MongoDB 4.x database