Changeset 1132 for extensions/net.sf.basedb.genepattern

Timestamp:

Jun 18, 2009, 2:26:04 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #234: Proof-of-concept: run a selected GenePattern? visualization module from BASE

This is a first attempt to run a visualization module. The main procedure is work and the really hard parts (starting the visualization applet with correct parameters and support files) have been done. But don't expect this to work outside of my development machine yet.

Location:

extensions/net.sf.basedb.genepattern/trunk

Files:

• META-INF/extensions.xml (modified) (1 diff)
• META-INF/servlets.xml (modified) (1 diff)
• resources/getFile.jsp (added)
• resources/test_visualizer.jsp (added)
• resources/visualizer.jsp (added)
• src/net/sf/basedb/genepattern/file/SupportFileTransferGateway.java (added)
• src/net/sf/basedb/genepattern/servlet/Visualizer.java (added)
• src/net/sf/basedb/genepattern/wrapper/GPClient.java (modified) (7 diffs)
• src/net/sf/basedb/genepattern/wrapper/SupportFileInfo.java (added)
• src/net/sf/basedb/genepattern/wrapper/TaskInfo.java (modified) (3 diffs)

extensions/net.sf.basedb.genepattern/trunk/META-INF/extensions.xml

@@ -59 +59 @@
     </action-factory>
   </extension>
+  <extension
+    id="net.sf.basedb.genepattern.visualizer"
+    extends="net.sf.basedb.clients.web.menu.extensions"
+    >
+    <index>4</index>
+    <about>
+      <name>Visualizer test</name>
+      <description>
+        A simple test of a visualizer
+      </description>
+    </about>
+    <action-factory>
+      <factory-class>
+        net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
+      </factory-class>
+      <parameters>
+        <title>Visualizer test&amp;hellip;</title>
+        <onClick>Main.openPopup('$HOME$/test_visualizer.jsp?ID='+getSessionId(), 'VisualizerTest', 500, 400)</onClick>
+        <icon>~/images/genepattern.gif</icon>
+      </parameters>
+    </action-factory>
+  </extension>
 </extensions>

extensions/net.sf.basedb.genepattern/trunk/META-INF/servlets.xml

@@ -10 +10 @@
   </servlet>
   <servlet>
+    <servlet-name>Visualizer</servlet-name>
+    <servlet-class>net.sf.basedb.genepattern.servlet.Visualizer</servlet-class>
+  </servlet>
+  <servlet>
     <servlet-name>Test</servlet-name>
     <servlet-class>net.sf.basedb.genepattern.servlet.Test</servlet-class>

extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/wrapper/GPClient.java

@@ -8 +8 @@
 import org.genepattern.webservice.AnalysisWebServiceProxy;
 import org.genepattern.webservice.Parameter;
+import org.genepattern.webservice.TaskIntegratorProxy;
 import org.genepattern.webservice.WebServiceException;
 
@@ -32 +33 @@
   private AdminProxy adminProxy;
   private AnalysisWebServiceProxy wsProxy;
+  private TaskIntegratorProxy tiProxy;
   
   /**
@@ -76 +78 @@
     class.
   */
-  protected AnalysisWebServiceProxy getAnalysisProxy()
+  public AnalysisWebServiceProxy getAnalysisProxy()
     throws WebServiceException
   {
@@ -91 +93 @@
     class.
   */
-  protected AdminProxy getAdminProxy()
+  public AdminProxy getAdminProxy()
     throws WebServiceException
   {
@@ -99 +101 @@
     }
     return adminProxy;
+  }
+  
+  public TaskIntegratorProxy getTaskIntegratorProxy()
+    throws WebServiceException
+  {
+    if (tiProxy == null)
+    {
+      tiProxy = new TaskIntegratorProxy(gpServer, login, password);
+    }
+    return tiProxy;
+    
   }
   
@@ -137 +150 @@
   }
 
+  public TaskInfo getTaskInfo(String module)
+    throws WebServiceException
+  {
+    org.genepattern.webservice.TaskInfo gpInfo = getAdminProxy().getTask(module);
+    return new TaskInfo(gpInfo);
+  }
+  
+  public SupportFileInfo[] getSupportFiles(String module)
+    throws WebServiceException
+  {
+    TaskIntegratorProxy tiProxy = getTaskIntegratorProxy();
+    
+    String[] fileNames = tiProxy.getSupportFileNames(module);
+    long[] dates = tiProxy.getLastModificationTimes(module, fileNames);
+    SupportFileInfo[] supportFiles = new SupportFileInfo[fileNames.length];
+    for (int i = 0; i < fileNames.length; ++i)
+    {
+      supportFiles[i] = new SupportFileInfo(fileNames[i], dates[i]);
+    }
+    return supportFiles;
+  }
+  
+  
   /**
     Get the input parameters for a module.
@@ -147 +183 @@
     throws WebServiceException
   {
-    org.genepattern.webservice.ParameterInfo[] gpParams = getGpClient().getParameters(module);
-    ParameterInfo[] parameters = new ParameterInfo[gpParams.length];
-    int index = 0;
-    for (int i = 0; i < gpParams.length; ++i)
-    {
-      ParameterInfo pi = new ParameterInfo(gpParams[i]);
-      if (filter == null || filter.evaluate(pi))
-      {
-        parameters[index] = pi;
-        index++;
-      }
-    }
-    return parameters;
+    TaskInfo ti = new TaskInfo(getAdminProxy().getTask(module));
+    return ti.getParameters(filter);
   }
   

extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/wrapper/TaskInfo.java

@@ -1 +1 @@
 package net.sf.basedb.genepattern.wrapper;
+
+import net.sf.basedb.util.filter.Filter;
 
 /**
@@ -76 +78 @@
     return value == null ? null : value.toString();
   }
+  
+  public String getAttribute(String key, String defaultValue)
+  {
+    Object value = getGPTaskInfo().getAttributes().get(key);
+    return value == null ? defaultValue : value.toString();
+  }
 
   /**
@@ -95 +103 @@
   }
   
+  public String getOs()
+  {
+    return getAttribute("os", "any");
+  }
   
+  public String getCpuType()
+  {
+    return getAttribute("cpuType", "any");
+  }
+  
+  public String getCommandLine()
+  {
+    return getAttribute("commandLine");
+  }
+  
+  public ParameterInfo[] getParameters(Filter<? super ParameterInfo> filter)
+  {
+    org.genepattern.webservice.ParameterInfo[] gpParams = gpInfo.getParameterInfoArray();
+    ParameterInfo[] parameters = new ParameterInfo[gpParams.length];
+    int index = 0;
+    for (int i = 0; i < gpParams.length; ++i)
+    {
+      ParameterInfo pi = new ParameterInfo(gpParams[i]);
+      if (filter == null || filter.evaluate(pi))
+      {
+        parameters[index] = pi;
+        index++;
+      }
+    }
+    return parameters;
+  }
   
 }