libSO

This is the version 0.1 of libSO. It provides a convenient way to read and write a PharmML standard output object (version 0.1) and it provides basic schema based validation.

Installation

Prerequisites

• Java JDK 1.6 or newer
• Ant (tested with version 1.8.4)

The project has been tested and is known to work with versions 1.6 and 1.7 of the JDK. Build instructions for both environments are provided below.

Setting up the project

If you are downloading this distribution from a git repository then you need to first clone the project to your local machine. The remote repository will typically tell you how to do this.

In the previous version, latest PharmML schema definitions were fetched from repository during the check-out process. This does not occur anymore as there is no more class auto-generated by XSD files, and we want stable definition files.

Java 6

1. First go to the build directory

   cd libPharmML

2. Fetch all dependencies using Ivy.

   ant retrieve

3. Force Java 6 use the latest version of JAXB instead of the one it comes with. This involves putting ivy_libs/src-build/jaxb-api.jar in your JRE's endorsed directory. You might use something like

   cp ivy_libs/src-build/jaxb-api.jar $JAVA_HOME/jre/lib/endorsed/

4. Build the jars. This should download all dependencies and then compile the code. You should end up with three jar files containing the binary code, the javadoc of the API and the src code.

   ant jar-all

Java 7

1. Navigate to the libPharmML folder: cd libPharmML

2. Open the Ant script and change the values of the properties source and target from 1.6 to 1.7.

3. Call the default ant target, jar-all:

   ant

Fetching libPharmML from Maven

libPharmML is available through the EBI Maven repository: url: http://www.ebi.ac.uk/~maven/m2repo/ group: eu.ddmore.pharmml module: libPharmML-SO version: 0.1-b1

Getting Started

Creating LibSO

	SOFactory soFactory = SOFactory.getInstance();
	LibSO libSO = soFactory.createLibSO();

Creating SO resource

	StandardisedOutputResource soResource = libSO.createDom(SOVersion.DEFAULT);

Starting populating the SO

	StandardisedOutput so = soResource.getDom();
	so.setImplementedBy("John Doe");

Adding a reference to the PharmML model

	so.createPharmMLRef("pharmml_model.xml");

Creating a SOBlock that will contain the results

	SOBlock block = so.createSoBlock();
	block.setBlkId("blk1");
	RawResults results = block.createRawResults();
    ImportDataType rawFile = results.createRawFile("oi1", "data/results.csv", "CSV", Delimiter.COMMA);
	// etc [...]

Validating the SO object

	IValidationReport valRep = libSO.getValidator().createValidationReport(soResource);
	for(int i=1;i<=valRep.numErrors();i++){
		System.err.println(valRep.getError(i));
	}

Saving the file

	libSO.save(new FileOutputStream("/homes/florent/tmp/so_out.xml"), soResource);

Credits

Florent Yvon.

22 Oct 2014.

Copyright EMBL-EBI 2014.