Changeset 3098

Timestamp:

Feb 5, 2007, 11:52:51 AM (17 years ago)

Author:

Nicklas Nordborg

Message:

References #10: Hierarchical clustering

Added servlet for downloading bioassay set data in Mev format

Location:

trunk

Files:

• build.xml (modified) (2 diffs)
• config/dist/web.xml (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/servlet/MevExport.java (added)
• src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (6 diffs)

trunk/build.xml

@@ -670 +670 @@
   <target
     name="web.init"
-    depends="core.init"
+    depends="core.init,coreplugins.init"
     >
     <property name="web.src" location="${src}/clients/web" 
@@ -681 +681 @@
       <path refid="core.classpath"/>
       <pathelement location="${core.build}"/>
+      <pathelement location="${coreplugins.build}" />
       <fileset dir="${lib}/servlet">
         <include name="**/*.jar"/>

trunk/config/dist/web.xml

@@ -127 +127 @@
   </servlet-mapping>
 
-  
+  <!-- The MevExport servlet used to download bioassay data to Mev -->
+  <servlet>
+    <servlet-name>mevexport</servlet-name>
+    <servlet-class>
+      net.sf.basedb.clients.web.servlet.MevExport
+    </servlet-class>
+  </servlet>
+  <servlet-mapping>
+    <servlet-name>mevexport</servlet-name>
+    <url-pattern>/plugins/org/tigr/microarray/mev/export</url-pattern>
+  </servlet-mapping>
+
   <!-- The CompileAll servlet used to compile all JSP pages -->
   <!-- EXPERIMENTAL!! -->

trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -78 +78 @@
 
 import java.io.IOException;
+import java.io.OutputStream;
 import java.io.PrintWriter;
 import java.sql.SQLException;
@@ -414 +415 @@
 
 
-  private void exportMeV(BioAssaySet bioassayset, File file,
+  public void exportMeV(BioAssaySet bioassayset, OutputStream to,
                          ProgressReporter progress)
     throws IOException, SQLException
   {
     DbControl dc=bioassayset.getDbControl();
-    PrintWriter out = new PrintWriter(file.getUploadStream(false));
+    PrintWriter out = new PrintWriter(to);
 
     // comment header
@@ -466 +467 @@
     }
 
-    progress.display(0, "Exporting ... performing database query");
+    if (progress != null) progress.display(0, "Exporting ... performing database query");
     // Reporter annotations and expression levels
     int nofchannels=bioassayset.getRawDataType().getChannels();
@@ -511 +512 @@
     while (spotData.hasNext())
     {
-      if (nof_processed_reporters%progress_report_interval == 0)
+      if (progress != null && (nof_processed_reporters%progress_report_interval == 0))
       {
         progress.display(100 * nof_processed_reporters / nof_reporters,
@@ -567 +568 @@
     }
     out.write("\n");
-
-    out.close();
+    out.flush();
   }
 
@@ -907 +907 @@
       // Add other export formats here
       String format = (String) job.getValue("fileformat");
-      if (format.equals(FORMAT_MEV)) exportMeV(bioassayset,file,progress);
+      if (format.equals(FORMAT_MEV)) 
+      {
+        OutputStream out = file.getUploadStream(false);
+        exportMeV(bioassayset, out, progress);
+        out.close();
+      }
       else if (format.equals(FORMAT_BASEFILE)) 
       {