Changeset 1119 for extensions/net.sf.basedb.genepattern

Timestamp:

Jun 10, 2009, 1:36:40 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #218: Proof-of-concept: run a selected GenePattern? module from BASE

Now uses a custom JSP page with some more interaction. Uses the new wrapper classes.

Location:

extensions/net.sf.basedb.genepattern/trunk

Files:

• resources/configure_plugin.jsp (added)
• src/net/sf/basedb/genepattern/GenePattern.java (modified) (2 diffs)
• src/net/sf/basedb/genepattern/plugin/GenePatternAnalysisPlugin.java (modified) (10 diffs)

extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/GenePattern.java

@@ -1 +1 @@
 package net.sf.basedb.genepattern;
+
+import net.sf.basedb.clients.web.extensions.ExtensionsControl;
+import net.sf.basedb.core.Presets;
+import net.sf.basedb.core.SessionControl;
 
 /**
@@ -36 +40 @@
   public static final String GCT_FILE = "genepattern.gct";
 
+  /**
+    Get the home directory URL for the GenePattern extension.
+  */
+  public static final String getHomeUrl()
+  {
+    return ExtensionsControl.getHomeUrl("net.sf.basedb.genepattern.options");
+  }
+    
 }

extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/plugin/GenePatternAnalysisPlugin.java

@@ -1 +1 @@
 package net.sf.basedb.genepattern.plugin;
 
-import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
-import java.util.Map;
-
-import org.genepattern.client.GPClient;
-import org.genepattern.webservice.JobResult;
+
 import org.genepattern.webservice.Parameter;
-import org.genepattern.webservice.ParameterInfo;
 import org.genepattern.webservice.WebServiceException;
 
@@ -25 +20 @@
 import net.sf.basedb.core.Experiment;
 import net.sf.basedb.core.File;
-import net.sf.basedb.core.FileParameterType;
-import net.sf.basedb.core.FloatParameterType;
-import net.sf.basedb.core.IntegerParameterType;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemQuery;
@@ -54 +46 @@
 import net.sf.basedb.core.signal.SignalTarget;
 import net.sf.basedb.core.signal.ThreadSignalHandler;
+import net.sf.basedb.genepattern.GPServer;
 import net.sf.basedb.genepattern.GenePattern;
 import net.sf.basedb.genepattern.file.BaseFileProxy;
 import net.sf.basedb.genepattern.file.FileTransferGateway;
-import net.sf.basedb.util.Enumeration;
-import net.sf.basedb.util.Values;
+import net.sf.basedb.genepattern.wrapper.GPClient;
+import net.sf.basedb.genepattern.wrapper.JobResult;
+import net.sf.basedb.genepattern.wrapper.ParameterInfo;
 
 public class GenePatternAnalysisPlugin 
@@ -122 +116 @@
       checkInterrupted();
       String gpModule = (String)configuration.getValue("gpModule"); 
-      Presets.Preset gpServer = getSelectedGpServer((String)job.getValue("gpServer"));
-      
-      GPClient gp = new GPClient(gpServer.getName(), 
-          gpServer.getSetting("server.login"), 
-          gpServer.getSetting("server.password"));
-      ParameterInfo[] info = gp.getParameters(gpModule);      
+      GPServer gpServer = GPServer.get(sc, (String)job.getValue("gpServer"));
+      
+      GPClient gp = new GPClient(gpServer);
+      ParameterInfo[] info = gp.getParameters(gpModule, null);      
       Parameter[] parameters = new Parameter[info.length];
       int index = 0;
@@ -163 +155 @@
       if (progress != null) 
       {
-        progress.display(25, "Running analysis on GenePattern server: " + gpServer.getName());
+        progress.display(25, "Running analysis on GenePattern server: " + gpServer.getUrl());
       }
       checkInterrupted();
       int jobId = gp.runAnalysisNoWait(gpModule, parameters);
       JobResult result = null;
-      while (true)
-      {
-        if (gp.isComplete(jobId))
-        {
-          result = gp.createJobResult(jobId);
-          break;
-        }
-        try
-        {
-          Thread.sleep(5000);
-        }
-        catch (InterruptedException ex)
-        {
-          throw new SignalException("Aborted by user");
-        }
-      }
-      
+      try
+      {
+        result = gp.waitFor(jobId, 5000);
+      }
+      catch (InterruptedException ex)
+      {
+        throw new SignalException("Aborted by user");
+      }
       checkInterrupted();
       
@@ -235 +218 @@
       {
         checkInterrupted();
-        URL url = result.getURLForFileName(f);
         File baseFile = File.getFile(dc, dir, f, true);
         if (!baseFile.isInDatabase()) dc.saveItem(baseFile);
@@ -488 +470 @@
     parameters.add(new PluginParameter<String>(
       "gpModule",
-      "GenePattern module/pipeline",
+      "Module/pipeline",
       "Enter the name or LSID of a GenePattern module or pipeline",
       new StringParameterType(255, null, true)
@@ -502 +484 @@
     configurePlugin = new RequestInformation(
       Request.COMMAND_CONFIGURE_PLUGIN,
-      "GenePattern module/pipeline",
+      "Configure GenePattern module/pipeline",
       "Select a GenePattern module or pipeline to run " +
       "when this configuration is selected.",
-      parameters
+      parameters,
+      GenePattern.getHomeUrl() + "/configure_plugin.jsp"
     );
     
-    
     return configurePlugin;
   }
@@ -517 +499 @@
     if (configureGpParameters != null) return configureGpParameters;
     String gpModule = (String)configuration.getValue("gpModule");
-    Presets.Preset gpServer = getSelectedGpServer(
+    GPServer gpServer = GPServer.get(sc,
         context == null ? (String)configuration.getValue("gpServer") : (String)job.getValue("gpServer"));
     
     try
     {
-      GPClient gp =  new GPClient(gpServer.getName(), 
-        gpServer.getSetting("server.login"), gpServer.getSetting("server.password"));
-      
-      ParameterInfo[] info = gp.getParameters(gpModule);
+      GPClient gp =  new GPClient(gpServer);
+      
+      ParameterInfo[] info = gp.getParameters(gpModule, null);
       List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>(info.length);
       
       for (ParameterInfo pi : info)
       {
-        PluginParameter<?> pp = convertToPluginParameter(pi, context != null);
-        if (pp != null) parameters.add(pp);
+        if (context != null || !pi.isInputFile())
+        {
+          PluginParameter<?> pp = pi.createPluginParameter("gp.");
+          if (pp != null) parameters.add(pp);
+        }
       }
       
@@ -569 +553 @@
   }
   
-  protected Presets.Preset getSelectedGpServer(String server)
-  {
-    String presetsXml = sc.getUserDefaultSetting("net.sf.basedb.genepattern.options");
-    System.out.println("xml=" + presetsXml);
-    Presets presets = new Presets();
-    if (presetsXml != null) presets.loadFrom(presetsXml);
-    return presets.getPreset(server);
-  }
-  
-  
-  protected PluginParameter<?> convertToPluginParameter(ParameterInfo pi, boolean forJob)
-  {
-    String name = pi.getName();
-    String type = (String)pi.getAttributes().get("type");
-    Map<String, String> choices = pi.getChoices();
-    PluginParameter<?> parameter = null;
-    if (pi.isInputFile())
-    {
-      if (forJob)
-      {
-        parameter = new PluginParameter<File>(
-          "gp." + name,
-          name,
-          pi.getDescription(),
-          new FileParameterType(null, !pi.isOptional(), 1)
-        );
-      }
-    }
-    else if (choices != null && !choices.isEmpty())
-    {
-      Enumeration<String, String> options = convertChoicesToEnumeration(choices);
-      parameter = new PluginParameter<String>(
-        "gp." + name,
-        name,
-        pi.getDescription(),
-        new StringParameterType(255, pi.getDefaultValue(), !pi.isOptional(), 1, 0, 0, options)
-      );
-    }
-    else if (type.equals("java.lang.String"))
-    {
-      parameter = new PluginParameter<String>(
-          "gp." + name,
-          name,
-          pi.getDescription(),
-          new StringParameterType(255, Values.getStringOrNull(pi.getDefaultValue()), !pi.isOptional())
-      );
-    }
-    else if (type.equals("java.lang.Integer"))
-    {
-      parameter = new PluginParameter<Integer>(
-        "gp." + name,
-        name,
-        pi.getDescription(),
-        new IntegerParameterType(null, null, 
-          Values.getInteger(pi.getDefaultValue(), null), !pi.isOptional())
-      );
-    }
-    else if (type.equals("java.lang.Float"))
-    {
-      parameter = new PluginParameter<Float>(
-        "gp." + name,
-        name,
-        pi.getDescription(),
-        new FloatParameterType(null, null, 
-          Values.getFloat(pi.getDefaultValue(), null), !pi.isOptional())
-      );
-    }
-    return parameter;
-  }
-  
-  protected Enumeration<String, String> convertChoicesToEnumeration(Map<String, String> choices)
-  {
-    if (choices == null || choices.isEmpty()) return null;
-    Enumeration<String, String> options = new Enumeration<String, String>();
-    for (Map.Entry<String, String> entry : choices.entrySet())
-    {
-      options.add(entry.getValue(), entry.getKey());
-    }
-    return options;
-  }
+  
 }