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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 6

The 2.31 and later versions of the library has been updated to work with Clarity 6, supporting version 2.31+ of the Clarity API. The opportunity has been taken to move things on with the client with this release. It is now based on Java 11 and is packaged with Java's module information. It has also provided a sensible time to do some repackaging, reflecting Genologics' disappearance as a separate company after its purchase by and absorbtion into Illumina.

  1. Anything in the packages below org.cruk.genologics is now under org.cruk.clarity.
  2. GenologicsAPI is now ClarityAPI, with the implementation classes also renamed.
  3. com.genologics.ri.process.GenologicsProcess is now com.genologics.ri.process.ClarityProcess.
  4. com.genologics.ri.file.GenologicsFile is now com.genologics.ri.file.ClarityFile.
  5. The Spring XML files are renamed from genologics-*.xml to clarity-*.xml.
  6. Any Spring beans in the configuration files prefixed with “genologics” are now prefixed with “clarity”, for example clarityAPIBase.

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.