Package org.fairdatapipeline.api

Java implementation of the FAIR Data Pipeline API

The main class for the FAIR Data Pipeline JAVA API is Coderun

Users should initialise this library using a try-with-resources block or ensure that .close() is explicitly closed when the required file handles have been accessed.

Usage example

    try (var coderun = new Coderun(configPath, scriptPath)) {
       ImmutableSamples samples = ImmutableSamples.builder().addSamples(1, 2, 3).rng(rng).build();
       String dataProduct = "animal/dodo";
       String component1 = "example-samples-dodo1";
       Data_product_write dp = coderun.get_dp_for_write(dataProduct, "toml");
       Object_component_write oc1 = dp.getComponent(component1);
       oc1.raise_issue("something is terribly wrong with this component", 10);
       oc1.writeSamples(samples);
     }
     

Class Summary

Class	Description
Coderun	Java implementation of the FAIR Data Pipeline API
Data_product	Data product is created: Coderun.get_dp_for_write(String, String) or Coderun.get_dp_for_read(String)
Data_product_read	Data_product_read is created by Coderun: Coderun.get_dp_for_read(String)
Data_product_write	Data_product_write is created by Coderun: Coderun.get_dp_for_write(String, String)
FileObject	A new registryObject with given storage_location, description, authors, file_type.
Issue	An issue that can be raised with objects or their components.
Object_component	This represents an object_component to read from or write to (or raise issues with) An object_component without a name is the 'whole_object' component.
Object_component_read	This represents an object_component to read from (or raise issues with) An object_component without a name is the 'whole_object' component.
Object_component_write	This represents an object_component to write to (or raise issues with) An object_component without a name is the 'whole_object' component.

Exception Summary

Exception	Description
IllegalActionException	The consumer is probably trying to do something they aren't supposed to be doing.
RegistryException	Failure to create an Object in the registry.
RegistryObjectNotfoundException	Failure to retrieve an expected object from the registry.