Running your code #

Below is a brief explanation how to make use of the Java FAIRDataPipeline library and actually getting your code to run from the FAIR CLI command line interface. The actual command to run your Java code is given in the script: line in the config.yaml. In my case I run the Java code using gradle run --args "${{CONFIG_DIR}}". You’ll have to change this if you don’t use gradle.

Below is an example config.yaml, stored in your projects /src/main/resources:

run_metadata:
  default_input_namespace: test
  description: Java test coderun
  script: |
    gradle run --args "${{CONFIG_DIR}}"

write:
- data_product: test/results/my-result
  description: test results

Your Java code then needs to read the registry token from the environment variable, and create a coderun using the config.yaml and script.sh files that will be placed in the CONFIG_DIR by FAIR CLI:

String token = System.getenv("FDP_LOCAL_TOKEN");
Path configFile = Path.of(args[0]).resolve("config.yaml");
Path scriptFile = Path.of(args[0]).resolve("script.sh");
try(var coderun = new Coderun(configPath, scriptPath, token)) {
	// create DP, Object_component, write results;
}

From your project root you can then just run the FAIR CLI commands:

fair init
fair pull src/main/resources/config.yaml
fair run src/main/resources/config.yaml