GenePattern Java Library
The GenePattern Java library allows you to invoke a GenePattern task as if it were a local Java method running on
your client and to get back from the task a list of result files. A zip file containing the Java library (and Javadoc that
describes the API for accessing the server and running tasks) is available on your GenePattern server.
To download the GenePattern Java library to your computer:
1. Start the GenePattern Web Client.
2. Under Programming Libraries in the right column, click the
zip link for the Java library.
3. After downloading the zip file, unzip it into the directory where you will be doing your Java development.
Running a Program
This section explores a simple Java application that preprocesses a dataset and displays it using the
HeatMapViewer. The included code can be copied and pasted into your Java program so that you can try it out,
modify it, and create your own solutions. The full source code of the sample application is available here.
The first statements in the application initialize various settings, which you must do once in every application that
accesses GenePattern. You will need to customize the italicized GenePattern server URL and GenePattern user
name (typically, your e-mail address) with values appropriate for your GenePattern server.
import org.genepattern.data.expr.ExpressionData;
import org.genepattern.client.GPServer;
import org.genepattern.webservice.JobResult;
import org.genepattern.webservice.Parameter;
import org.genepattern.io.IOUtil;
import java.io.File;
public class MyProgram {
public static void main(String[] args)
throws Exception {
GPServer gpServer=new GPServer("http://localhost:8080",
"your email address");
After initializing the required settings, the application runs the PreprocessDataset task to preprocess a dataset. This
example references the dataset using a publicly-accessible URL, but a filename would be equally valid. When you
invoke the
runAnalysis method, the GenePattern library invokes the appropriate task on the server, passing all of
the input parameters and input files. Control returns to your application when the task completes. (To run a task
asynchronously, invoke the runAnalysis method in a separate thread.)
String inputDataset=
"ftp://ftp.broad.mit.edu/pub/genepattern/all_aml/all_aml_train.res";
JobResult preprocess
=gpServer.runAnalysis("PreprocessDataset",
new Parameter[] {
new Parameter("input.filename", inputDataset)
});
When the task completes, you can query the JobResult object for an array of filenames that are the output from
the task. You can download the result files or leave them on the server and refer to them by URL. Referring to result
files by URL is especially useful for intermediate results. In this example, the
JobResult object named
preprocess contains a list of filenames (of length 1, in this case), which the application displays in a heat map:
// view results in a HeatMapViewer visualizer
17
gpServer.runVisualizer("HeatMapViewer",
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