Gradle

Tasks

Task Name	Description
bootRun	Runs the Spring Boot application
bootJar	Creates an executable jar
bootWar	Creates an executable war
test	Run all tests of the application

Run tasks

To run gradle task, enter

./gradlew {task_name}

Documentation

• Spring Boot Gradle Plugin Reference Guide
  
• The Java Plugin documentation
  
• The War Plugin documentation
  

Configuration

Configuration stored in src/main/resources/application.yml:

server:
  port:
    8080
ignite:
  addresses:
    127.0.0.1:8446, 127.0.0.2:8446
  clientPort:
    8443
  restPort:
    8444
  communicationSPIPort:
    8445
  discoverySPIPort:
    8446
  storage:
    /opt/data
  addToBaselineTopology:
    true

logging:
  file: ./logs.log
  level:
    enrichmentapi.calc: DEBUG

Available parameters

Parameter	Meaning	Default
server.port	Enrichment API port	8080
ignite.addresses	list of Ignite nodes
ignite.clientPort	Client connector port (JDBC Thin port)	10800
ignite.communicationSPIPort	Communication SPI port	47100
ignite.discoverySPIPort	Discovery SPI port	47500
ignite.restPort	REST access port	11211
ignite.storage	Location of Ignite files
ignite.addToBaselineTopology	Add node to baseline topology	false
logging.file	Path to log file

Documentation

• Ignite documentation
  

Docker

To run Enrichment API in a Docker container host network has to be used, otherwise Ignite nodes won't be able to create cluster. Also all described above ports have to be available between cluster instances.

Example:

docker run --rm -d \
           --network=host \            # using host network
           -v /opt/data:/opt/data \    # bind mount of Ignite data direcotry
           --name=enrichmentapi \
           enrichmentapi

Docker compose

To deploy application as part of Compose cluster could be used next configuration:

...

data-api:
  build: ./data-api
  network_mode: "host"        # host network
  volumes:
    - /opt/data:/opt/data     # Ignite data directory
...

Also could be useful to add alias to enrichmentAPI host:

extra_hosts:
  - "data-api:10.0.0.1"

Activation of Ignite cluster

When the application is launched for the first time, the Ignite cluster must be activated. This must be done only once.

To activate Ignite cluster, make a call to GET /api/v1/activate.

Upload of data from SO files to Ignite

POST /api/v1/download-so

{
	"datasetType": "geneset_library" or "rank_matrix",
	"fileName": "path/to/so/file",
	"name": "name of the dataset (e.g. creeds_uid)"
}

If you want to upload files into docker version of EnrichmentAPI ensure that fileName (path to file) is available inside a container. For example, you can mount directory with SO files inside the container and specify fileName accordingly.

Swagger

Description of API available on /swagger-ui.html