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CRUK-CI Clarity API Java Client

The Cancer Research UK Cambridge Institute (CRUK-CI) Clarity Java Client provides the Java or Groovy developer a means to work with Clarity's REST API using objects rather than XML or DOM document trees.

It provides a single interface to perform (almost) all the operations supported by the Clarity REST API with XML to Java object conversion, error handling and, optionally, client side caching. The developer works with Java objects that map onto the XML documents described by Illumina's API documentation.

It uses the JAXB object to XML binding mechanism to convert the XML messages sent to and received from Clarity's REST API. The communication uses Apache's HTTP Java client and Spring's REST client. Spring is used throughout this tool.

Features

  1. Automatic conversion between XML and Java objects.
  2. Automatic handling of exceptions from the server.
  3. Automatic and transparent use of batch retrieve, update and create mechanisms where available.
  4. Creation of files with the upload to the file store (likewise file removal).
  5. Optional transparent caching mechanism.
  6. Debugging classes to show traffic and timings between the client and server.

Clarity Client version 2

Version 2 of the client is a port of the original project updated to work with Jakarta EE10. It is written for Java 17 and has embraced the Java 9+ module system. It is also refactored to be a multi-module project for Maven with the model classes derived from the XML schemas now in their own artefact and the cache also moved into its own artefact, allowing a more modular use of the code. The artifacts and modules are:

  1. clarity-client2-model: The model classes derived from the schemas and annotated for serialisation with JAXB. The Java module for these classes is com.genologics.ri.
  2. clarity-client2: The main client classes, Java module org.cruk.clarity.api.
  3. clarity-client2-cache: The caching classes and configuration, Java module org.cruk.clarity.api.cache.
  4. clarity-client2-recorder: The recording and playback classes to support repeatable unit tests, Java module org.cruk.clarity.api.recorder.
  5. clarity-client2-filestore-mina: An SFTP file store implementation using Apache Mina SSHD as the underlying library.
  6. clarity-client2-filestore-jsch: An SFTP file store implementation using JCraft JSch as the underlying library.

The client has kept the com.genologics.ri namespace for the model classes because that namespace is still what is used in the XSD files provided by Illumina. It follows from the namespace that the Java module for these classes is therefore com.genologics.ri.