Changeset 3469

Timestamp:

Jun 8, 2007, 4:54:32 PM (16 years ago)

Author:

Johan Enell

Message:

Fixes #606
Fixes #622

Location:

branches/2.3.1/src/plugins/core/net/sf/basedb/plugins

Files:

• Base1PluginExecuter.java (modified) (14 diffs)
• BioAssaySetExporter.java (modified) (1 diff)

branches/2.3.1/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -72 +72 @@
 import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.util.Enumeration;
-import net.sf.basedb.util.RemovableUtil;
 import net.sf.basedb.util.XMLUtil;
 import net.sf.basedb.util.parser.FlatFileParser;
@@ -469 +468 @@
       try
       {
-        id = Directory.getIdFromPath(dc, path);
         // delete existing
-        RemovableUtil.removeRecursively(dc, Item.DIRECTORY, Collections.singleton(id), true);
+        deleteDir(dc, path);
         dc.commit();
         dc = sc.newDbControl();
@@ -513 +511 @@
     return dir.delete();
   }
-    
+  
+  
+  /**
+   * Deletes all files and subdirectories under dir.
+   * 
+   * @param dc
+   * @param dirId
+   * @return Returnes true if all deletions were succssful
+   */
+  private boolean deleteDir(DbControl dc, Path dir)
+  {
+    if (dir.getType() == Path.Type.DIRECTORY)
+    {
+      Directory d = Directory.getByPath(dc, dir);
+      for (File f : d.getFiles().list(dc))
+      {
+        dc.deleteItem(f);
+      }
+      for (Directory subD : d.getSubDirectories().list(dc))
+      {
+        if (!deleteDir(dc, subD.getPath()))
+        {
+          return false;
+        }
+      }
+      try
+      {
+        dc.deleteItem(d);
+        return true;
+      }
+      catch(BaseException e)
+      {
+        return false;
+      }
+    }
+    return false;
+  }
 
   @Override
@@ -559 +593 @@
     if (command.equals(Request.COMMAND_EXECUTE))
     {
-      DbControl dc = sc.newDbControl();
-      int tId = -1;
+      DbControl dc = null;
       try
       {
+        dc = sc.newDbControl();
         getManualConfigureParameters();
         getConfigureJobParameters();
-        progress.display(0, "Exporting data to be used by plugin.");
-        File stdin = exportData(dc);
-        copy(stdin, getExecDirectory());
+  
+        Transformation trans = null;
+        File stdin = null;
         
+        //Export
+        try
+        {
+          BioAssaySet parentBas = getSourceBioAssaySet(dc);
+          trans = parentBas.newTransformation(Job.getById(dc, job.getId()));
+          trans.setName(PluginConfiguration.getById(dc, configuration.getId()).getName());
+          dc.saveItem(trans);
+          progress.display(0, "Exporting data to be used by plugin.");
+          stdin = File.getById(dc, exportData());
+  
+          copy(stdin, getExecDirectory());
+        }
+        catch(Exception e)
+        {
+          response.setError("Error during export", Arrays.asList(e));
+          return;
+        }
         
-        progress.display(10, "Running on remote computation server.");
-        Process p = Runtime.getRuntime().exec(getExecLine(), null, getExecDirectory());
-
-        ByteArrayOutputStream err = new ByteArrayOutputStream();
-        StreamHandler errorStream = new StreamHandler(new BufferedInputStream(p.getErrorStream()), new BufferedOutputStream(err));
-
-        FileOutputStream out = new FileOutputStream(new java.io.File(getExecDirectory(), "stdout.txt"));
-        StreamHandler inputStream = new StreamHandler(new BufferedInputStream(p.getInputStream()), new BufferedOutputStream(out));
-        
-        StreamHandler outputStream = new StreamHandler(new BufferedInputStream(stdin.getDownloadStream(0)), new BufferedOutputStream(p.getOutputStream()));
-        
-        inputStream.start();
-        errorStream.start();
-        outputStream.start();
-        int exitValue = p.waitFor();
-        err.flush();
-        out.close();
-        
-        if (exitValue == 0)
+        //Execution
+        String msg = "";
+        try
+        {
+          progress.display(10, "Running on remote computation server.");
+          Process p = Runtime.getRuntime().exec(getExecLine(), null, getExecDirectory());
+  
+          ByteArrayOutputStream err = new ByteArrayOutputStream();
+          StreamHandler errorStream = new StreamHandler(new BufferedInputStream(p.getErrorStream()), new BufferedOutputStream(err));
+  
+          FileOutputStream out = new FileOutputStream(new java.io.File(getExecDirectory(), "stdout.txt"));
+          StreamHandler inputStream = new StreamHandler(new BufferedInputStream(p.getInputStream()), new BufferedOutputStream(out));
+          
+          FileInputStream in = new FileInputStream(new java.io.File(getExecDirectory(), "stdin.txt"));
+          StreamHandler outputStream = new StreamHandler(new BufferedInputStream(in), new BufferedOutputStream(p.getOutputStream()));
+          
+          inputStream.start();
+          errorStream.start();
+          outputStream.start();
+          int exitValue = p.waitFor();
+
+          for(int i = 0; errorStream.isAlive(); ++i)
+          {
+            Thread.sleep(1000);
+            if (i > 300) throw new BaseException("Waited 5 minutes for the errormessage. I give up.");
+          }
+                    
+          err.flush();
+          msg = err.toString();
+          out.flush();
+          
+          if (exitValue != 0)
+          {
+            response.setError(msg, null);
+            return;
+          }
+          else
+          {
+            response.setDone(msg);
+          }
+        }
+        catch (Exception e)
+        {
+          response.setError("Error during execution", Arrays.asList(e));
+          return;
+        }
+        finally
+        {
+          //Copy files
+          dc.deleteItem(stdin);
+          importFiles(dc, trans);
+          if (!deleteDir(getExecDirectory()))
+          {
+            response.setError("Could not remove execution directory: "+getExecDirectory().getAbsolutePath(), null);
+          }
+        }
+              
+        //Import data
+        try
         {
           progress.display(70, "Importing data from plugin.");
-          tId = importData();
-          response.setDone(err.toString());
-        }
-        else
-        {
-          BioAssaySet parentBas = getSourceBioAssaySet(dc);
-          Transformation trans = parentBas.newTransformation(Job.getById(dc, job.getId()));
-          trans.setName(getTransformationName(dc));
-          dc.saveItem(trans);
+          importData(dc, trans);
+          response.setDone(msg);
+        }
+        catch (Exception ex)
+        {
+          response.setError(ex.getMessage(), Arrays.asList(ex));
+          return;
+        }
+      }
+      finally
+      {
+        if (dc != null)
+        {
           dc.commit();
-          tId = trans.getId();
-          response.setError("Process ended with error: " + exitValue + "\n" + err, null);
-        }
-      }
-      catch (IOException ex)
-      {
-        response.setError(ex.getMessage(), Arrays.asList(ex));
-      }
-      catch (InterruptedException ex)
-      {
-        response.setError(ex.getMessage(), Arrays.asList(ex));
-      }
-      finally
-      {
-        if (dc != null)
           dc.close();
-        if (tId != -1)
-          importFiles(tId);
-        if (!deleteDir(getExecDirectory()))
-        {
-          response.setError("Could not remove execution directory: "+getExecDirectory().getAbsolutePath(), null);
         }
       }
@@ -638 +713 @@
    * @return The file where the data is exported to.
    */
-  private File exportData(DbControl dc)
-  {
+  private int exportData()
+  {
+    DbControl dc = null;
     try
     {
+      dc = sc.newDbControl();
       Directory d = getPluginDirectory(dc);
       File file = File.getFile(dc, d, "stdin.txt", true);
       file.setMimeTypeAuto("text/plain", null);
-      if(!file.isInDatabase()) dc.saveItem(file);
+      dc.saveItem(file);
       
       BioAssaySet bas = getSourceBioAssaySet(dc);
@@ -667 +744 @@
       
       Map<String, String> parameters = new HashMap<String, String>();
-      for (PluginParameter<?> pp : getJobParameters())
+      for (PluginParameter<?> pp : getJobParametersFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName()))))
       {
         String name = pp.getName();
@@ -683 +760 @@
         exporter.exportBaseFileMatrix(bas, file, parameters, reporterFields, spotFields, mergeReporters);
       }
-      return file;
+      dc.commit();
+      return file.getId();
     }
     catch (IOException e)
@@ -692 +770 @@
     {
       throw new BaseException(e);
+    }
+    finally
+    {
+      if (dc != null)
+        dc.close();
     }
   }
@@ -706 +789 @@
   {
     DbControl dc = null;
-    List<AnnotationType> list = null;
+    List<AnnotationType> list = new ArrayList<AnnotationType>();
     try
     {
       dc = sc.newDbControl();
       Experiment e = super.getCurrentExperiment(dc);
-      ItemQuery<AnnotationType> query = e.getExperimentalFactors();
-      query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
-      query.order(Orders.asc(Hql.property("name")));
-      list = query.list(dc);
+      if (e != null)
+      {
+        ItemQuery<AnnotationType> query = e.getExperimentalFactors();
+        query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+        query.order(Orders.asc(Hql.property("name")));
+        list = query.list(dc);
+      }
     }
     finally
@@ -1104 +1190 @@
    * @throws IOException if there is any error reading from stdou.txt
    */
-  private int importData()
+  private int importData(DbControl dc, Transformation t)
     throws IOException
   {
-//    int posCnt = 0;
-    DbControl dc = null;
-    Transformation t = null;
-
-    try
-    {
-      dc = sc.newDbControl();
-      Job jobitem = Job.getById(dc, job.getId());
-      BioAssaySet parentBas = getSourceBioAssaySet(dc);
-      t = parentBas.newTransformation(jobitem);
-      t.setName(getTransformationName(dc));
-      dc.saveItem(t);
-      
-      BioAssaySet bas = null;
-      SpotBatcher spotBatcher = null;
-      PositionBatcher posBatcher = null;
-  
-      HashMap<String, BioAssay> idMap = new HashMap<String, BioAssay>();
-      HashMap<Integer, Integer> posMap = new HashMap<Integer, Integer>();
-      HashMap<String, ExtraValueType> evtMap = new HashMap<String, ExtraValueType>();
-  
-      FlatFileParser ffp = getInitializedFlatFileParser(new FileInputStream(new java.io.File(getExecDirectory(), "stdout.txt")));
-      
-      while (ffp.hasMoreSections())
-      {
-        FlatFileParser.Line section = ffp.nextSection();
-        ffp.parseHeaders();
+    BioAssaySet bas = null;
+    SpotBatcher spotBatcher = null;
+    PositionBatcher posBatcher = null;
+
+    HashMap<String, BioAssay> idMap = new HashMap<String, BioAssay>();
+    HashMap<Integer, Integer> posMap = new HashMap<Integer, Integer>();
+    HashMap<String, ExtraValueType> evtMap = new HashMap<String, ExtraValueType>();
+
+    File stdout = File.getFile(dc, getPluginDirectory(dc), "stdout.txt", true);
+    FlatFileParser ffp = getInitializedFlatFileParser(stdout.getDownloadStream(0));
+    
+    while (ffp.hasMoreSections())
+    {
+      FlatFileParser.Line section = ffp.nextSection();
+      ffp.parseHeaders();
+      
+      if (section.name().equals("assays"))
+      {
+        bas = t.newProduct(null, "new", false);
+        bas.setName(getSourceBioAssaySet(dc).getName());
+
+        List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
+        int idCol = columns.indexOf("id");
+        int nameCol = columns.indexOf("name");
+        int parentCol = columns.indexOf("parents");
+
+        ffp.setMinDataColumns(columns.size());
+
+        FlatFileParser.Data dataline = ffp.nextData();
+        while (dataline != null)
+        {
+          String id = dataline.get(idCol);
+          String name = dataline.get(nameCol);
+          Set<BioAssay> baParents;
+          if (parentCol > -1)
+          {
+            String[] parentIds;
+            parentIds = dataline.get(parentCol).split("/");
+            baParents = new HashSet<BioAssay>(parentIds.length);
+            for (String parent : parentIds)
+            {
+              baParents.add(BioAssay.getById(dc, new Integer(parent)));
+            }
+          }
+          else
+          {
+            try
+            {
+              baParents = Collections.singleton(BioAssay.getById(dc, Integer.parseInt(id)));
+            }
+            catch (ItemNotFoundException e)
+            {
+              throw new BaseException("Couldn't find any parent for bioassay "+name, e);
+            }
+          }
+          BioAssay ba = bas.newBioAssay(baParents);
+          ba.setName(name);
+          idMap.put(id, ba);
+          dataline = ffp.nextData();
+        }
+      }
+      else if (section.name().equals("spots"))
+      {
+        List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
+        List<String> assays = Arrays.asList(ffp.getHeader("assays").split("\\t"));
+        List<String> assayFields = Arrays.asList(ffp.getHeader("assayFields").split("\\t"));
+        List<String> setExtraFloats = new ArrayList<String>(); 
+        if (ffp.getHeader("setExtraFloats") != null)
+          setExtraFloats = Arrays.asList(ffp.getHeader("setExtraFloats").split("\\t"));
         
-        if (section.name().equals("assays"))
-        {
-          bas = t.newProduct("new", "new", false);
-          bas.setName(getSourceBioAssaySet(dc).getName());
-  
-          List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
-          int idCol = columns.indexOf("id");
-          int nameCol = columns.indexOf("name");
-          int parentCol = columns.indexOf("parents");
-  
-          ffp.setMinDataColumns(columns.size());
-  
-          FlatFileParser.Data dataline = ffp.nextData();
-          while (dataline != null)
-          {
-            String id = dataline.get(idCol);
-            String name = dataline.get(nameCol);
-            Set<BioAssay> baParents;
-            if (parentCol > -1)
+        if (bas == null)
+        {
+          bas = t.newProduct(null, "new", false);
+        }
+        spotBatcher = bas.getSpotBatcher();
+//        posBatcher = bas.getPositionBatcher();
+
+        for (String assayId : assays)
+        {
+          if (idMap.get(assayId) == null)
+          {
+            try
             {
-              String[] parentIds;
-              parentIds = dataline.get(parentCol).split("/");
-              baParents = new HashSet<BioAssay>(parentIds.length);
-              for (String parent : parentIds)
-              {
-                baParents.add(BioAssay.getById(dc, new Integer(parent)));
-              }
+              BioAssay parent = BioAssay.getById(dc, Integer.parseInt(assayId));
+              BioAssay ba = bas.newBioAssay(parent);
+              idMap.put(assayId, ba);
             }
-            else
+            catch (ItemNotFoundException e)
             {
-              try
-              {
-                baParents = Collections.singleton(BioAssay.getById(dc, Integer.parseInt(id)));
-              }
-              catch (ItemNotFoundException e)
-              {
-                throw new BaseException("Couldn't find any parent for bioassay "+name);
-              }
+              throw new BaseException("Couldn't find any parent for bioassay "+assayId);
             }
-            BioAssay ba = bas.newBioAssay(baParents);
-            ba.setName(name);
-            idMap.put(id, ba);
-            dataline = ffp.nextData();
-          }
-        }
-        else if (section.name().equals("spots"))
-        {
-          List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
-          List<String> assays = Arrays.asList(ffp.getHeader("assays").split("\\t"));
-          List<String> assayFields = Arrays.asList(ffp.getHeader("assayFields").split("\\t"));
-          List<String> setExtraFloats = new ArrayList<String>(); 
-          if (ffp.getHeader("setExtraFloats") != null)
-            setExtraFloats = Arrays.asList(ffp.getHeader("setExtraFloats").split("\\t"));
-          
-          if (bas == null)
-          {
-            bas = t.newProduct(null, "new", false);
-          }
-          spotBatcher = bas.getSpotBatcher();
-          posBatcher = bas.getPositionBatcher();
-  
-          for (String assayId : assays)
-          {
-            if (idMap.get(assayId) == null)
-            {
-              try
-              {
-                BioAssay parent = BioAssay.getById(dc, Integer.parseInt(assayId));
-                BioAssay ba = bas.newBioAssay(parent);
-                idMap.put(assayId, ba);
-              }
-              catch (ItemNotFoundException e)
-              {
-                throw new BaseException("Couldn't find any parent for bioassay "+assayId);
-              }
-            }
-          }
-          
-          ffp.setMinDataColumns(columns.size() - 1 + assays.size() * assayFields.size());
-          
-          boolean intCols = true;
-  
-          int posCol = columns.indexOf("position");
-          int repCol = columns.indexOf("reporter");
-          int dataCol = columns.indexOf("assayData");
-          int[] intCol = new int[bas.getRawDataType().getChannels()];
-          for (int i = 0; i < intCol.length; ++i)
-          {
-            int col = assayFields.indexOf("intensity"+(i+1));
-            if (col != -1)
-            {
-              intCol[i] = col;
-            }
-            else
-            {
-              intCols = false;
-            }
-          }
-          int mCol = assayFields.indexOf("l2ratio1_2");
-          int aCol = assayFields.indexOf("l10intgmean1_2");
-          int[] extraFloatsCol = new int[setExtraFloats.size()];
-  
-          if (dataCol > -1)
-          {
-            if (!intCols && (mCol > -1 && aCol > -1))
-            {
-              intCols = false;
-            }
-            else if (!intCols)
+          }
+        }
+        
+        ffp.setMinDataColumns(columns.size() - 1 + assays.size() * assayFields.size());
+        
+        boolean intCols = true;
+
+        int posCol = columns.indexOf("position");
+        int repCol = columns.indexOf("reporter");
+        int dataCol = columns.indexOf("assayData");
+        int[] intCol = new int[bas.getRawDataType().getChannels()];
+        for (int i = 0; i < intCol.length; ++i)
+        {
+          int col = assayFields.indexOf("intensity"+(i+1));
+          if (col != -1)
+          {
+            intCol[i] = col;
+          }
+          else
+          {
+            intCols = false;
+          }
+        }
+        int mCol = assayFields.indexOf("l2ratio1_2");
+        int aCol = assayFields.indexOf("l10intgmean1_2");
+        int[] extraFloatsCol = new int[setExtraFloats.size()];
+
+        if (dataCol > -1)
+        {
+          if (!intCols && (mCol > -1 && aCol > -1))
+          {
+            intCols = false;
+          }
+          else if (!intCols)
+          {
+            throw new BaseException(
+              "Can't find the intensity column(s) or l2ratio1_2/l10intgmean1_2. No data could be imported.");
+          }
+          for (int i = 0; i < setExtraFloats.size(); i++)
+          {
+            int col = assayFields.indexOf(setExtraFloats.get(i));
+            if (col < 0)
             {
               throw new BaseException(
-                "Can't find the intensity column(s) or l2ratio1_2/l10intgmean1_2. No data could be imported.");
+                "Can't find the column " + setExtraFloats.get(i) + ". No data could be inmported.");
             }
-            for (int i = 0; i < setExtraFloats.size(); i++)
+            extraFloatsCol[i] = col + dataCol;
+          }
+        }
+        else
+        {
+          throw new BaseException("Can't find the column 'assayData' in header assayFields.");
+        }
+
+        for (int i = 0; i < intCol.length; ++i)
+          intCol[i] += dataCol;
+        aCol += dataCol;
+        mCol += dataCol;
+        
+        List<SpotExtraValueBatcher<Float>> evBatcher = new ArrayList<SpotExtraValueBatcher<Float>>(setExtraFloats.size());
+        for (int i = 0; i < setExtraFloats.size(); i++)
+        {
+          String name = setExtraFloats.get(i);
+          ExtraValueType evt = evtMap.get(name);
+          if (evt == null)
+          {
+            try
             {
-              int col = assayFields.indexOf(setExtraFloats.get(i));
-              if (col < 0)
+              evt = ExtraValueType.getByExternalId(dc, name);
+            }
+            catch (ItemNotFoundException e)
+            {
+              evt = ExtraValueType.getNew(dc, name, Type.FLOAT);
+              evt.setName(name);
+              dc.saveItem(evt);
+            }
+            evtMap.put(name, evt);
+          }
+          evBatcher.add(i, bas.getSpotExtraValueBatcher(Float.class, evt, Job.getById(dc, job.getId())));
+        }
+        
+        while (ffp.hasMoreData())
+        {
+          FlatFileParser.Data dataline = ffp.nextData();
+          int index = 0;
+          for (String assayId : assays)
+          {
+            BioAssay ba = idMap.get(assayId);
+            try
+            {
+              float[] intensities = new float[intCol.length];
+              Integer reporter = dataline.get(repCol) == null ? null : new Integer(dataline.get(repCol));
+              Integer position = dataline.get(posCol) == null ? null : new Integer(dataline.get(posCol));
+
+              if (intCols)
               {
-                throw new BaseException(
-                  "Can't find the column " + setExtraFloats.get(i) + ". No data could be inmported.");
+                for (int i = 0; i < intCol.length; ++i)
+                  intensities[i] = dataline.get(intCol[i] + index) == null ? Float.NaN : new Float(dataline.get(intCol[i] + index));
               }
-              extraFloatsCol[i] = col + dataCol;
+              else
+              {
+                float a = dataline.get(aCol + index) == null ? Float.NaN : new Float(dataline.get(aCol + index));
+                float m = dataline.get(mCol + index) == null ? Float.NaN : new Float(dataline.get(mCol + index));
+
+                // int2 = 10^a / 2^(0.5*m)
+                // int1 = int2 * 2^m
+                intensities[1] = new Float(Math.pow(10, a) / Math.pow(2, 0.5 * m));
+                intensities[0] = new Float(intensities[1] * Math.pow(2, m));
+              }
+
+              spotBatcher.insert(ba.getDataCubeColumnNo(), position, intensities);
+              
+//              if (posMap.containsKey(position))
+//              {
+//                if (!posMap.get(position).equals(reporter))
+//                  throw new BaseException("Invalid data. Position, "+position+", occures twice with different reporter data.");
+//                
+//              }
+//              else
+//              {
+//                posMap.put(position, reporter);
+//                posBatcher.insert(position, Reporter.getById(dc, reporter));
+//              }
+              for (int i = 0; i < evBatcher.size(); i++)
+              {
+                try
+                {
+                  Float ev = new Float(dataline.get(extraFloatsCol[i] + index));
+                  evBatcher.get(i).insert(ba.getDataCubeColumnNo(), position, ev);
+                }
+                catch (NumberFormatException e)
+                {}
+              }
+              index += assayFields.size();
             }
-          }
-          else
-          {
-            throw new BaseException("Can't find the column 'assayData' in header assayFields.");
-          }
-  
-          for (int i = 0; i < intCol.length; ++i)
-            intCol[i] += dataCol;
-          aCol += dataCol;
-          mCol += dataCol;
-          
-          List<SpotExtraValueBatcher<Float>> evBatcher = new ArrayList<SpotExtraValueBatcher<Float>>(setExtraFloats.size());
-          for (int i = 0; i < setExtraFloats.size(); i++)
-          {
-            String name = setExtraFloats.get(i);
-            ExtraValueType evt = evtMap.get(name);
-            if (evt == null)
-            {
-              try
-              {
-                evt = ExtraValueType.getByExternalId(dc, name);
-              }
-              catch (ItemNotFoundException e)
-              {
-                evt = ExtraValueType.getNew(dc, name, Type.FLOAT);
-                evt.setName(name);
-                dc.saveItem(evt);
-              }
-              evtMap.put(name, evt);
-            }
-            evBatcher.add(i, bas.getSpotExtraValueBatcher(Float.class, evt, jobitem));
-          }
-          
-          while (ffp.hasMoreData())
-          {
-            FlatFileParser.Data dataline = ffp.nextData();
-            int index = 0;
-            for (String assayId : assays)
-            {
-              BioAssay ba = idMap.get(assayId);
-              try
-              {
-                float[] intensities = new float[intCol.length];
-                Integer reporter = dataline.get(repCol) == null ? null : new Integer(dataline.get(repCol));
-                Integer position = dataline.get(posCol) == null ? null : new Integer(dataline.get(posCol));
-  
-                if (intCols)
-                {
-                  for (int i = 0; i < intCol.length; ++i)
-                    intensities[i] = dataline.get(intCol[i] + index) == null ? Float.NaN : new Float(dataline.get(intCol[i] + index));
-                }
-                else
-                {
-                  float a = dataline.get(aCol + index) == null ? Float.NaN : new Float(dataline.get(aCol + index));
-                  float m = dataline.get(mCol + index) == null ? Float.NaN : new Float(dataline.get(mCol + index));
-  
-                  // int2 = 10^a / 2^(0.5*m)
-                  // int1 = int2 * 2^m
-                  intensities[1] = new Float(Math.pow(10, a) / Math.pow(2, 0.5 * m));
-                  intensities[0] = new Float(intensities[1] * Math.pow(2, m));
-                }
-  
-                spotBatcher.insert(ba.getDataCubeColumnNo(), position, intensities);
-                
-                if (posMap.containsKey(position))
-                {
-                  if (!posMap.get(position).equals(reporter))
-                    throw new BaseException("Invalid data. Position, "+position+", occures twice with different reporter data.");
-                  
-                }
-                else
-                {
-                  posMap.put(position, reporter);
-                  posBatcher.insert(position, Reporter.getById(dc, reporter));
-                }
-                for (int i = 0; i < evBatcher.size(); i++)
-                {
-                  try
-                  {
-                    Float ev = new Float(dataline.get(extraFloatsCol[i] + index));
-                    evBatcher.get(i).insert(ba.getDataCubeColumnNo(), position, ev);
-                  }
-                  catch (NumberFormatException e)
-                  {}
-                }
-                index += assayFields.size();
-              }
-              catch (NumberFormatException e)
-              {}
-            }
-          }
-        }
-      }
-      // save bas
-      if (bas != null)
-      {
-        dc.saveItem(bas);
-        for (BioAssay ba : idMap.values())
-        {
-          dc.saveItem(ba);
-        }
-      }
-      dc.commit();
-    }
-    finally
-    {
-      if (dc != null)
-        dc.close();
+            catch (NumberFormatException e)
+            {}
+          }
+        }
+      }
+    }
+    // save bas
+    if (bas != null)
+    {
+      dc.saveItem(bas);
+      for (BioAssay ba : idMap.values())
+      {
+        dc.saveItem(ba);
+      }
     }
     
@@ -1374 +1441 @@
   
 
-  private void importFiles(int transformationId)
-  {
-    DbControl dc = null;
+  private void importFiles(DbControl dc, Transformation trans)
+  {
+    DbControl mydc = null;
     try
     {
-      dc = sc.newDbControl();
-      Directory homeDirectory = getPluginDirectory(dc);
-      importTempFiles(dc, getExecDirectory().listFiles(), homeDirectory);
-      dc.commit();
-      dc.close();
-      
-      dc = sc.newDbControl();
-      Transformation t = Transformation.getById(dc, transformationId);
-      for(File f : homeDirectory.getFiles().list(dc))
-      {
-        AnyToAny ata = AnyToAny.getNew(dc, t, f, f.getPath().toString(), false);
-        dc.saveItem(ata);
-      }
-      for(Directory d : homeDirectory.getSubDirectories().list(dc))
-      {
-        AnyToAny ata = AnyToAny.getNew(dc, t, d, d.getPath().toString(), false);
-        dc.saveItem(ata);
-      }
-      dc.commit();
+      mydc = sc.newDbControl();
+      Directory homeDirectory = getPluginDirectory(mydc);
+      importTempFiles(mydc, getExecDirectory().listFiles(), homeDirectory);
+      mydc.commit();
     }
     finally
     {
-      if (dc != null)
-      {
-        dc.close();
-      }
+      if (mydc != null)
+        mydc.close();
+    }
+    
+    Directory homeDirectory = getPluginDirectory(dc);
+    for(File f : homeDirectory.getFiles().list(dc))
+    {
+      AnyToAny ata = AnyToAny.getNew(dc, trans, f, f.getPath().toString(), false);
+      dc.saveItem(ata);
+    }
+    for(Directory d : homeDirectory.getSubDirectories().list(dc))
+    {
+      AnyToAny ata = AnyToAny.getNew(dc, trans, d, d.getPath().toString(), false);
+      dc.saveItem(ata);
     }
   }
@@ -1438 +1500 @@
         importTempFiles(dc, f.listFiles(), newDirectory);
       }
-      f.delete();
     }
   }
@@ -1667 +1728 @@
           StringParameterType t = new StringParameterType(255, defaultValue, true, 1, new Integer(options), 1, enums);
           parameter = new PluginParameter<String>(name, commonName, "", t);
-          jobParameters.add(parameter);
           break;
         }
@@ -1680 +1740 @@
       }
       return parameter;
+    }
+    
+    public final String getCommonName()
+    {
+      return commonName;
+    }
+
+    public final String getDefaultValue()
+    {
+      return defaultValue;
+    }
+
+    public final Enumeration<String, String> getEnumOptions()
+    {
+      return enumOptions;
+    }
+
+    public final String getName()
+    {
+      return name;
+    }
+
+    public final String getOptions()
+    {
+      return options;
+    }
+
+    public final int getPosition()
+    {
+      return position;
+    }
+
+    public final boolean isRemoved()
+    {
+      return removed;
+    }
+
+    public final Base1JobParameterType getType()
+    {
+      return type;
     }
 

branches/2.3.1/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -262 +262 @@
     if (!parameters.isEmpty())
     {
-      for (String key : parameters.keySet())
+      Set<String> keys = new HashSet<String>(parameters.keySet());
+      if (keys.remove("section"))
+      {
+        out.println("section\t"+parameters.get("section"));
+      }
+      for (String key : keys)
       {
         out.println(key+"\t"+parameters.get(key));