Changeset 1118 for extensions/net.sf.basedb.genepattern

Timestamp:

Jun 10, 2009, 1:21:51 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #229: Implement API for additional GenePattern? web services

The test servlet now use the wrapper classes when possible.

File:

• extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/servlet/Test.java (modified) (4 diffs)

extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/servlet/Test.java

@@ -29 +29 @@
 import javax.servlet.http.HttpServletResponse;
 
-import org.genepattern.client.GPClient;
-import org.genepattern.webservice.JobResult;
 import org.genepattern.webservice.Parameter;
-import org.genepattern.webservice.WebServiceException;
+import org.genepattern.webservice.TaskInfoAttributes;
 
 import net.sf.basedb.clients.web.Base;
-import net.sf.basedb.core.Application;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.File;
@@ -42 +39 @@
 import net.sf.basedb.genepattern.file.BaseFileProxy;
 import net.sf.basedb.genepattern.file.FileTransferGateway;
-import net.sf.basedb.util.FileUtil;
-import net.sf.basedb.util.StaticCache;
+import net.sf.basedb.genepattern.wrapper.GPClient;
+import net.sf.basedb.genepattern.wrapper.JobResult;
+import net.sf.basedb.genepattern.wrapper.ParameterInfo;
+import net.sf.basedb.genepattern.wrapper.TaskInfo;
 
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.PrintWriter;
-import java.io.Writer;
 import java.net.URL;
 
@@ -93 +90 @@
 
       GPClient gp = new GPClient(GP_HOME, GP_LOGIN, GP_PWD);
-      JobResult result = gp.runAnalysis(
+      //AdminProxy ap = new AdminProxy(GP_HOME, GP_LOGIN, GP_PWD);
+      
+      TaskInfo[] tasks = gp.getModules(null);
+      PrintWriter out = response.getWriter();
+      out.println("<b>Tasks</b><br>");
+      for (TaskInfo ti : tasks)
+      {
+        org.genepattern.webservice.TaskInfo gpTi = ti.getGPTaskInfo();
+        TaskInfoAttributes tia = gpTi.getTaskInfoAttributes();
+        out.println("name="+ti.getName()+"<br>");
+        out.println("access_id="+gpTi.getAccessId()+"<br>");
+        out.println("descr="+ti.getDescription()+"<br>");
+        out.println("ID="+gpTi.getID()+"<br>");
+        out.println("lsid="+ti.getLsid()+"<br>");
+        out.println("shortname="+gpTi.getShortName()+"<br>");
+        out.println("userid="+gpTi.getUserId()+"<br>");
+        out.println("containsinputfileparam="+gpTi.containsInputFileParam()+"<br>");
+        out.println("pipeline="+ti.isPipeline()+"<br>");
+        out.println("attr="+gpTi.getAttributes()+"<br>");
+        out.println("tiattr="+tia+"<br>");
+        out.println("toString=" + ti.toString());
+        out.println("<hr>");
+      }
+      out.flush();
+
+      
+      ParameterInfo[] info = gp.getParameters("urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00044:5", null);
+      //PrintWriter out = response.getWriter();
+      out.println("<b>Parameters</b><br>");
+      for (ParameterInfo pi : info)
+      {
+        org.genepattern.webservice.ParameterInfo gpPi = pi.getGPParameterInfo();
+        out.println("name="+pi.getName()+"<br>");
+        out.println("label="+pi.getLabel()+"<br>");
+        out.println("descr="+pi.getDescription()+"<br>");
+        out.println("default="+pi.getDefaultValue()+"<br>");
+        out.println("choices="+pi.getChoices()+"<br>");
+        out.println("attr="+gpPi.getAttributes()+"<br>");
+        out.println("optional="+pi.isOptional()+"<br>");
+        out.println("inputfile="+pi.isInputFile()+"<br>");
+        out.println("outputfile="+gpPi.isOutputFile()+"<br>");
+        out.println("password="+gpPi.isPassword()+"<br>");
+        out.println("toString=" + pi.toString());
+        out.println("<hr>");
+      }
+      out.flush();
+      
+      int jobId = gp.runAnalysisNoWait(
         "urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00044:5", 
         new Parameter[]{
@@ -110 +154 @@
           new Parameter("output.filename", "<input.file_basename>.comp.marker.odf")
         });
-      
-      
+      JobResult result = gp.waitFor(jobId, 5000);
+      org.genepattern.webservice.JobResult gpJr = result.getGPJobResult();
       String[] files = result.getOutputFileNames();
-      PrintWriter out = response.getWriter();
+      out.println("<p><b>Result files:</b><br>");
       for (String f : files)
       {
-        URL url = result.getURL(f);
-        out.print("<a href=\"" + url + "\" target=\"_new\">" + f + ": " + url + "</a><br>");
+        URL url = gpJr.getURL(f);
+        out.println("<a href=\"" + url + "\" target=\"_new\">" + f + ": " + url + "</a><br>");
       }
 
     }
-    catch (WebServiceException ex)
+    catch (Exception ex)
     {
       throw new ServletException(ex);