Changeset 998

Timestamp:

Mar 27, 2009, 11:05:43 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Addresses #118 and #183. Moved export of data to an export method.

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/qQuantileNormalization.java (modified) (3 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/qQuantileNormalization.java

@@ -52 +52 @@
 import java.io.FileReader; // Jari, remove this?
 import java.io.IOException;
+import java.io.PrintWriter; // Jari, remove this?
 import java.sql.SQLException;
 import java.util.EnumSet;
@@ -101 +102 @@
 
 
+
+  // This function will be rewritten when the BASE core plug-in
+  // BioAssaySetExporter is refactored, see tickets
+  // http://base.thep.lu.se/ticket/742,
+  // http://base.thep.lu.se/ticket/1256, and
+  // http://baseplugins.thep.lu.se/ticket/183.
+  private void exportData()
+    throws IOException
+  {
+    if (debug_output) System.err.println("qQN: exportData()");
+    FileOutputStream os = new FileOutputStream(new File(getExecDirectory(),
+                                                        subprocess_stdin));
+    BioAssaySetExporter base=new BioAssaySetExporter();
+    try
+    {
+      base.exportPlainMatrix(sourceBAS, os, null);
+    }
+    catch (SQLException e)
+    {
+      e.printStackTrace();
+//      response.setError(e.getMessage(), Arrays.asList(e));
+    }
+
+    // creating a meta-data file to track the information in the plain
+    // matrix file created above. This will be removed when BASE
+    // BioAssaySetExporter is refactored. Of course, the current
+    // meta-data file is highly specific for the needs here, but this
+    // use case should be covered hete. Or, way not fall back on a
+    // BASEfile?
+
+    // The query must be the same as the one done in BASE core plug-in
+    // BioAssaySetExporter::exportPlainMatrix. This will be removed
+    // when http://base.thep.lu.se/ticket/1256 and consequently
+    // http://baseplugins.thep.lu.se/ticket/183 are fixed.
+    DbControl dc=sc.newDbControl();
+    DynamicSpotQuery query=sourceBAS.getSpotData();
+    query.select(Dynamic.select(VirtualColumn.POSITION));
+    query.select(Dynamic.select(VirtualColumn.COLUMN));
+    int nof_channels=sourceBAS.getRawDataType().getChannels();
+    for (int i=1; i<=nof_channels; ++i)
+      query.select(Dynamic.select(VirtualColumn.channel(i)));
+    query.order(Orders.asc(Dynamic.column(VirtualColumn.POSITION)));
+    query.order(Orders.asc(Dynamic.column(VirtualColumn.COLUMN)));
+    try {
+      DynamicResultIterator spotData = query.iterate(dc);
+      int column_position=spotData.getIndex(VirtualColumn.POSITION.getName());
+      int[] column_channel=new int[nof_channels];
+      for (int i=0; i<nof_channels; ++i)
+        column_channel[i]=spotData.getIndex(VirtualColumn.channel(i+1).getName());
+
+      PrintWriter output = new PrintWriter(getExecDirectory() +
+                                           java.io.File.separator + metadata);
+
+      // first line in meta data is assay column numbers in BASE data cube
+      List<BioAssay> sourceAssays = sourceBAS.getBioAssays().list(dc);
+      int nofAssays=sourceAssays.size();
+      for (int i=0; i<nofAssays; ++i)
+      {
+        if (i>0) output.print('\t');
+        output.print(sourceAssays.get(i).getDataCubeColumnNo());
+      }
+      output.println();
+
+      // write positions needed for storing result in BASE.
+      int position=0;
+      while (spotData.hasNext())
+      {
+        int prev_position=position;
+        SqlResult item = spotData.next();
+        position=item.getInt(column_position);
+        if (position!=prev_position) output.println(position);
+      }
+      output.close();
+    }
+    catch (SQLException e)
+    {
+//      response.setError(e.getMessage(), Arrays.asList(e));
+      throw new BaseException(e);
+    }
+    finally 
+    {
+      if (dc != null)
+        dc.close();
+    }
+  }
+
+
   protected void runBinary()
     throws InterruptedException, IOException
   {
-    if (debug_output) System.err.println("runBinary(qQN)");
-    try
-    {
-      subprocess_stdin="in.data";
-      subprocess_stdout="out.data";
-      FileOutputStream os = new FileOutputStream(new File(getExecDirectory(),
-                                                          subprocess_stdin));
-      BioAssaySetExporter base=new BioAssaySetExporter();
-      base.exportPlainMatrix(sourceBAS, os, null);
-      String[] cmd = { "qQN" };
-      execute(cmd);
-    }
-    catch (SQLException e)
-    {
-      e.printStackTrace();
-//      response.setError(e.getMessage(), Arrays.asList(e));
-    }
+    if (debug_output) System.err.println("qQN: runBinary()");
+    subprocess_stdin="in.data";
+    subprocess_stdout="out.data";
+    metadata="meta.data";
+    exportData();
+    String[] cmd = { "qQN" };
+    execute(cmd);
   }
 
@@ -146 +224 @@
       SpotBatcher batcher = child.getSpotBatcher();
 
-      // The query must be the same as the one done in BASE core
-      // plug-in BioAssaySetExporter::exportPlainMatrix. This will be
-      // removed when http://base.thep.lu.se/ticket/1256 and
-      // consequently http://baseplugins.thep.lu.se/ticket/183 are
-      // fixed.
-      DynamicSpotQuery query=sourceBAS.getSpotData();
-      query.select(Dynamic.select(VirtualColumn.POSITION));
-      query.select(Dynamic.select(VirtualColumn.COLUMN));
-      int nof_channels=sourceBAS.getRawDataType().getChannels();
-      for (int i=1; i<=nof_channels; ++i)
-        query.select(Dynamic.select(VirtualColumn.channel(i)));
-      query.order(Orders.asc(Dynamic.column(VirtualColumn.POSITION)));
-      query.order(Orders.asc(Dynamic.column(VirtualColumn.COLUMN)));
-      DynamicResultIterator spotData = query.iterate(dc);
-      int column_position=spotData.getIndex(VirtualColumn.POSITION.getName());
-      int[] column_channel=new int[nof_channels];
-      for (int i=0; i<nof_channels; ++i)
-        column_channel[i]=spotData.getIndex(VirtualColumn.channel(i+1).getName());
-
-      List<BioAssay> sourceAssays = sourceBAS.getBioAssays().list(dc);
-      int nofAssays=sourceAssays.size();
-      short[] column=new short[nofAssays];
-      for (int i=0; i<nofAssays; ++i)
-        column[i]=sourceAssays.get(i).getDataCubeColumnNo();
-
+      BufferedReader metainput =
+        new BufferedReader(new FileReader(getExecDirectory() +
+                                          java.io.File.separator + metadata));
       BufferedReader input =
         new BufferedReader(new FileReader(getExecDirectory() +
                                           java.io.File.separator +
                                           subprocess_stdout));
-      String line;
-      int position=0;
-      while ((line = input.readLine()) != null)
+
+      // first line in meta data is assay column numbers in BASE data cube
+      String inputline=metainput.readLine();
+      String[] lineSplit = inputline.split("\\s");
+      Short[] column=new Short[lineSplit.length];
+      for (int i=0; i<lineSplit.length; ++i)
+        column[i]=Short.parseShort(lineSplit[i]);
+      while ((inputline = input.readLine()) != null)
       {
-        int prev_position=position;
-        while (position==prev_position)
-        {
-          if (!spotData.hasNext())
-            throw new BaseException("File/database size mismatch");
-          SqlResult item = spotData.next();
-          position=item.getInt(column_position);
-        }
-        String[] lineSplit = line.split("\\s");
-        if (lineSplit.length != nofAssays)
+        lineSplit = inputline.split("\\s");
+        if (lineSplit.length != column.length)
           throw new BaseException("File/bioassay set size mismatch");
-        for (int i=0; i<nofAssays; ++i)
+        if ((inputline = metainput.readLine()) == null)
+          throw new BaseException("Data and result file size mismatch");
+        int position = Integer.parseInt(inputline);
+        for (int i=0; i<column.length; ++i)
         {
           // C/C++ style string nan's (Java expects NaN) will cause a