Providing your own meta data provider

What is a meta data provider

this is nothing else than a tool which provides BinBase with meta data related to a specific sample/class/experiment and provides the possibility to store results.

General procedure

This is a fairly simple procedure.

implement an interface
create a factory class
pack it up and deploy it
register your service

Implementing the interface.

Please implement this interface. You can find our reference implementation here.

package edu.ucdavis.genomics.metabolomics.binbase.bci.setupX;

import edu.ucdavis.genomics.metabolomics.exception.BinBaseException;

public interface SetupXProvider{

	public String getSetupXId(String sampleName) throws BinBaseException;

	public String getMetaInformationByClass(String setupXId) throws BinBaseException;
	public String getMetaInformationBySample(String setupXId) throws BinBaseException;
	public String getMetaInformationByExperiment(String setupXId) throws BinBaseException;
	public void upload(String experimentId, String content) throws BinBaseException;
}

How should the output look like for BinBase of your provider

Currently we are only using 3 methods of the metadata provider in BinBase since more is not needed. These methods are

getSetupXId
getMetainformationBySample
upload

The method "getSetupXId" just return the unique id for the given sampleName as a plain string. An example would be

12312312

The "upload" method expects the id for the current experiment and a string containing the binary data for the upload. The binaery date will represent a zip archive which contains more data. This means you need to convert the retrieved data on your site into a byte array and store somewhere. We know that this is ugly, but it's related to historical code.

The Method "getMetainformationBySample" is the most important method and has to return a specific xml string in this format. We will integrate an XSD for this in the future. An example would be:

generated by setupx!

<sample>
  <classInfo>
    <atom key="Species">Arabidopsis thaliana</atom>
    <atom key="Genotype">Wild type Col0: 1</atom>
  </classInfo>
  <runInfo>
    <atom key="Type">Sample</atom>
    <atom key="Folder">Acquired Samples</atom>
    <atom key="MSMethod">343605</atom>
    <atom key="DPMethod">85</atom>
    <atom key="Name">020222byusa100</atom>
    <atom key="tray">1</atom>
    <atom key="QC Method">Gas Chromatograph (GC) Methods quick-splitless_working</atom>
    <atom key="ASMethod">Mass Spectrometer (MS) Methods quick_1700V</atom>
    <atom key="GCMethod">Data Processing (DP) Methods fiehn default</atom>
    <atom key="Vial" />
  </runInfo>
  <genericInfo>
    <atom key="Sample ID">343605</atom>
    <atom key="Class ID">343626</atom>
    <atom key="Experiment ID">343581</atom>
    <atom key="filename">070719byusa300:1</atom>
    <atom key="label">WtCol04:1-1</atom>
    <atom key="comment">Wild type Col-0 Mutant Experiment #4 sample 1-1</atom>
  </genericInfo>
</sample>

generated by the binbase scheduler

<sample>
  <classInfo>
    <atom key='Species'>not specified</atom>
    <atom key='Genotype'>not specified</atom>
    <atom key='Organ'>not specified</atom>
  </classInfo>
  <genericInfo>
    <atom key='Sample ID'>1</atom>
    <atom key='Class ID'>1</atom>
    <atom key='Experiment ID'>1</atom>
    <atom key='filename'>test</atom>
  </genericInfo>
  <runInfo>
    <atom key='Type'>Sample</atom>
    <atom key='Folder'>unknown</atom>
    <atom key='MSMethod'>unknown</atom>
    <atom key='Name'>test</atom>
    <atom key='tray'>1</atom>
    <atom key='QC Method'>unknown</atom>
    <atom key='ASMethod'>unknown</atom>
    <atom key='GCMethod'>unknown</atom>
    <atom key='Vial' />
    <atom key='Owner'>test</atom>
  </runInfo>
</sample>

This is basically the smalles accepted xml code.

Creating the factory class.

Once the interface is implemented you need to write a factory class for it which needs to be extended from this class.

/**
	 * creates the provider itself
	 *
	 * @author wohlgemuth
	 * @version Nov 17, 2005
	 * @return
	 */
	public abstract SetupXProvider createProvider(Properties p);

Packing it up and deployment

once you got your implementation done and wrote the factory you need to pack your classes in a way that the application server can load them. The easiest way is to create a jar archive and deploy it as an ejb3 file

register you service

finally you need to register your server with the correct JMX bean.

Domain Name:binbase
service: MetaProvider
MBean Java Class: edu.ucdavis.genomics.metabolomics.binbase.bci.server.jmx.MetaProviderJMX

You can use the jmx-console for this or can use the api.

provide your own meta data provider