The package org.biomoby.shared.parser contains classes for parsing Biomoby data from an XML format (a Biomoby XML envelope) into Java objects, and back to XML.

The parser itself is in the class {@link org.biomoby.shared.parser.MobyParser MobyParser} that is accompanied by a list of all Biomoby's XML tags and attribute names stored in the {@link org.biomoby.shared.parser.MobyTags MobyTags} class.

Java objects representing parsed data start with {@link org.biomoby.shared.parser.MobyPackage MobyPackage} - the main container (that also invokes parser itself). A MobyPackage instance corresponds to one network call to a Biomoby service, or to a response from such service.

Here is a full example how to get parsed Biomoby XML data into a MobyPackage (note that the input XML - the variable data in the example - can be given as a String, byte[], or a File which conveniently corresponds with the requirement from the Biomoby API):

  try {
      MobyPackage mobyInput = MobyPackage.createFromXML (data);

      // here do something with 'mobyInput'

  } catch (MobyException e) {
      System.out.println (e.getMessage());
  }

To bring data back into XML is again simple:

  try {
      // fill response data into a mobyOutput...
      MobyPackage mobyOutput = new MobyPackage();
      ...

      // and convert it into XML
      String xml = mobyOutput.toXML();

  } catch (MobyException e) {
      System.out.println (e.getMessage());
  }

A MobyPackage then contains one or more {@link org.biomoby.shared.parser.MobyJob MobyJob}s each of them containing one "execution" (or a "query" in a Biomoby speak). Note that a Biomoby service must be able to accept more invocations (jobs, queries) from one network request. A MobyJob can also carry a response from a service. Again, data coming from a service can consist from more responses - actually the number of the MobyJob objects in a response must be exactly the same as a number of the MobyJob objects in the originated request.

A MobyJob has the data themselves - they are either stored in {@link org.biomoby.shared.parser.MobySimple MobySimple}s or in {@link org.biomoby.shared.parser.MobyCollection MobyCollection}s. The number and types of these {@link org.biomoby.shared.parser.MobyDataElement MobyDataElement}s are defined for each Biomoby service in a Biomoby registry.

The MobySimples have data stored in various data objects - their classes are in the package {@link org.biomoby.shared.datatypes}. The primitive data types are there available directly, the other types can be generated (see details in the package itself).

Here is a picture showing how the entities are relates:

Data containers for parsed data