Changeset 3108

Timestamp:

Feb 6, 2007, 3:28:34 PM (16 years ago)

Author:

Johan Enell

Message:

BASE1PluginExecuter uses BioAssaySetExporter? to create basefile

File:

• trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (33 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -21 +21 @@
  Foundation, Inc., 59 Temple Place - Suite 330,
  Boston, MA  02111-1307, USA.
- */
+*/
 
 package net.sf.basedb.plugins;
@@ -34 +34 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Directory;
-import net.sf.basedb.core.DynamicResultIterator;
-import net.sf.basedb.core.DynamicSpotQuery;
 import net.sf.basedb.core.Experiment;
 import net.sf.basedb.core.ExtraValue;
@@ -44 +42 @@
 import net.sf.basedb.core.Include;
 import net.sf.basedb.core.IntegerParameterType;
-import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemNotFoundException;
-import net.sf.basedb.core.ItemParameterType;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Job;
@@ -60 +56 @@
 import net.sf.basedb.core.SpotExtraValueBatcher;
 import net.sf.basedb.core.StringParameterType;
-import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.Transformation;
 import net.sf.basedb.core.Type;
-import net.sf.basedb.core.User;
-import net.sf.basedb.core.VirtualColumn;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
-import net.sf.basedb.core.plugin.AbstractPlugin;
+import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
 import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.core.plugin.InteractivePlugin;
+import net.sf.basedb.core.plugin.Permissions;
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
-import net.sf.basedb.core.query.Dynamic;
-import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
-import net.sf.basedb.core.query.JoinType;
 import net.sf.basedb.core.query.Orders;
-import net.sf.basedb.core.query.Restrictions;
-import net.sf.basedb.core.query.Select;
-import net.sf.basedb.core.query.Selects;
-import net.sf.basedb.core.query.SqlResult;
-import net.sf.basedb.core.query.WhenStatement;
-import net.sf.basedb.util.BioAssaySetUtil;
 import net.sf.basedb.util.Enumeration;
+import net.sf.basedb.util.RemovableUtil;
 import net.sf.basedb.util.parser.FlatFileParser;
 
@@ -100 +86 @@
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
+import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -109 +97 @@
 import java.util.regex.Pattern;
 
-public class Base1PluginExecuter extends AbstractPlugin implements InteractivePlugin
+public class Base1PluginExecuter extends AbstractAnalysisPlugin implements InteractivePlugin
 {
   /**
@@ -122 +110 @@
     null,
     "http://base.thep.lu.se");
-
-  private static final Set<GuiContext> guiContexts = Collections.singleton(new GuiContext(Item.BIOASSAYSET, GuiContext.Type.ITEM));
-
+ 
+  private static final Set<Permissions> permissions = new HashSet<Permissions>();
+  
   /**
    * Parameter definition that asks for the file that should be imported. This
@@ -132 +120 @@
     "file",
     "File",
-    "The file to import the data from",
-    new FileParameterType(null, true, 1));
+    "The file to import the data from. If you leave this parameter blank you can manually configure the plug-in.",
+    new FileParameterType(null, false, 1));
 
   private static PluginParameter<String> execPathParameter = new PluginParameter<String>(
@@ -140 +128 @@
     "The path to the executables",
     new StringParameterType(255, null, true));
-
-  /** File configuration parameters * */
-  private static final String serialFormatParameterName = "serialFormat";
-
-  private static final String versionNumberParameterName = "versionNumber";
-
-  private static final String execNameParameterName = "execName";
-
-  private static final String geneAveragesParameterName = "geneAverages";
-
-  private static final String minChannelsParameterName = "minChannels";
-
-  private static final String maxChannelsParameterName = "maxChannels";
-
-  private static final String leaveStdinParameterName = "leaveStdin";
-
-  private static final String leaveStdoutParameterName = "leaveStdout";
-
-  private static final String usedColumnsParameterName = "usedColumns";
-
-  private static final String usedFieldsParameterName = "usedFields";
-
-  /** * */
-
-  /** Job parameters * */
-  private static final PluginParameter<BioAssaySet> bioAssaySetParameter = new PluginParameter<BioAssaySet>(
-    "bioAssaySet",
-    "Bioassay set",
-    "The bioassay set that this plugin will run on",
-    new ItemParameterType<BioAssaySet>(BioAssaySet.class, null, true, 1, null));
-
-  private static final String pluginDirectoryParameterName = "pluginDirectory";
-
-  /** **/
-
-  private static final String PARSE_CONFIG_FILE = "PARSE_CONFIG_FILE";
+  
+  /* File configuration parameters */
+  private PluginParameter<Boolean> serialFormatParameter;
+  private PluginParameter<String> versionNumberParameter;
+  private PluginParameter<String> execNameParameter;
+  private PluginParameter<Boolean> geneAveragesParameter;
+  private PluginParameter<Integer> minChannelsParameter;
+  private PluginParameter<Integer> maxChannelsParameter;
+  private PluginParameter<Boolean> leaveStdinParameter;
+  private PluginParameter<Boolean> leaveStdoutParameter;
+  private PluginParameter<String> usedColumnsParameter;
+  private PluginParameter<String> usedFieldsParameter;
+  
+  /* Job parameters */
+  private PluginParameter<String> pluginDirectoryParameter;
+
+  private static final String COMMAND_MANUAL_CONFIG = "COMMAND_MANUAL_CONFIG";
 
   private RequestInformation configureJob;
-
   private RequestInformation configurePlugin;
-
-  private RequestInformation configureFile;
+  private RequestInformation configureManual;
 
   /**
@@ -189 +156 @@
 
   /**
-   * This list holds the configure parameters derived from the headers in the
-   * configuration file.
-   */
-  private List<PluginParameter<?>> configureFileParameters;
-
-  /**
    * This is the directory where the plugin will generate its output.
    */
   private java.io.File execDirectory;
 
-  private Directory pluginDirectory;
-
-  private Map<String, Select> base1columns = null;
-
-  // *** From InteractivePlugin iterface
-  public Set<GuiContext> getGuiContexts()
-  {
-    return guiContexts;
-  }
-
+  /* From InteractivePlugin iterface */
+
+  @Override
   public String isInContext(GuiContext context, Object item)
   {
-    String message = null;
-    if (item == null)
-    {
-      message = "The object is null";
-    }
-    else if (!(item instanceof BioAssaySet))
-    {
-      message = "The object is not a BioAssaySet: " + item;
-    }
-    else
-    {
-      DbControl dc = sc.newDbControl();
-      RequestInformation ri = getConfigureFileParameters();
-
-      PluginConfiguration pc = PluginConfiguration.getById(dc, configuration.getId()); 
-      String name = pc.getName();
-      
-      BioAssaySet bas = (BioAssaySet) item;
-
-      int channels = bas.getRawDataType().getChannels();
-      Integer maxChannels = pc.getParameterValues(maxChannelsParameterName).isEmpty() ? null : (Integer) pc.getParameterValues(maxChannelsParameterName).get(0);
-      Integer minChannels = (Integer) pc.getParameterValues(minChannelsParameterName).get(0);
-      if (channels < minChannels || ( maxChannels != 0 && channels > maxChannels))
-      {
-        message = name + " can't work on " + channels + "-channel data. " + minChannels + " < " + channels + " < " + maxChannels;
-      }
-      
-      List<String> extraValues = new ArrayList<String>();
-      for (ExtraValue ev : bas.getExtraValues().list(dc))
-      {
-        extraValues.add(ev.getExtraValueType().getName());
-      }
-      Pattern p = Pattern.compile("_xc_(.+)\\t?");
-      Matcher m = p.matcher((String) ri.getParameter(usedFieldsParameterName).getParameterType().getDefaultValue());
-      while (message == null && m.find())
-      {
-        if (!extraValues.contains(m.group(1)))
-        {
-          message = "Requires "+ m.group(1) +" attached to BioAssaySet";
-        }
-      }
-      dc.close();
+    String message = super.isInContext(context, item);
+    if (message == null)
+    {
+      DbControl dc = null;
+      try
+      {
+        dc = sc.newDbControl();
+        getManualConfigureParameters();
+
+        BioAssaySet bas = (BioAssaySet) item;
+        int channels = bas.getRawDataType().getChannels();
+        Integer maxChannels = (Integer) configuration.getValue(maxChannelsParameter.getName());
+        Integer minChannels = (Integer) configuration.getValue(minChannelsParameter.getName());;
+        if (channels < minChannels || ( maxChannels != 0 && channels > maxChannels))
+        {
+          message = configuration.getPluginConfiguration().getName() + " can't work on " + channels + "-channel data. " + minChannels + " < " + channels + " < " + maxChannels;
+        }
+        
+        List<String> extraValues = new ArrayList<String>();
+        for (ExtraValue ev : bas.getExtraValues().list(dc))
+        {
+          extraValues.add(ev.getExtraValueType().getName());
+        }
+        Pattern p = Pattern.compile("_xc_(.+)\\t?");
+        Matcher m = p.matcher((CharSequence) configuration.getValue(usedFieldsParameter.getName()));
+        while (message == null && m.find())
+        {
+          if (!extraValues.contains(m.group(1)))
+          {
+            message = "Requires "+ m.group(1) +" attached to BioAssaySet";
+          }
+        }
+      }
+      catch (Exception e)
+      {
+        message = e.getMessage();
+        e.printStackTrace();
+      }
+      finally
+      {
+        if (dc != null)
+        {
+          dc.close();
+        }
+      }
     }
     return message;
@@ -266 +223 @@
       requestInformation = getConfigurePluginParameters();
     }
-    else if (command.equals(Base1PluginExecuter.PARSE_CONFIG_FILE))
-    {
-      requestInformation = getConfigureFileParameters();
+    else if (command.equals(Base1PluginExecuter.COMMAND_MANUAL_CONFIG))
+    {
+      requestInformation = getManualConfigureParameters();
     }
     else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
@@ -278 +235 @@
       catch (IOException e)
       {
-        throw new BaseException("Unable to configure job from configuratin file.");
-      }
+        throw new BaseException("Unable to configure job from configuration file. "+e.getMessage());
+      }
+    }
+    else
+    {
+      throw new BaseException("Unknown command: "+command);
     }
     return requestInformation;
   }
+  
 
   public void configure(GuiContext context, Request request, Response response)
   {
     String command = request.getCommand();
+    DbControl dc = null;
     try
     {
       if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
       {
+        storeValue(configuration, request, execPathParameter);
         storeValue(configuration, request, fileParameter);
-        storeValue(configuration, request, execPathParameter);
-
-        response.setContinue(Base1PluginExecuter.PARSE_CONFIG_FILE);
-      }
-      else if (command.equals(Base1PluginExecuter.PARSE_CONFIG_FILE))
-      {
-        for (PluginParameter<?> p : getConfigureParameters())
-        {
-          storeValue(configuration, request, p);
-        }
-
+        
+        dc = sc.newDbControl();
+        File f = (File) request.getParameterValue(fileParameter.getName());
+        PluginConfiguration pc = PluginConfiguration.getById(dc, configuration.getId());
+        if (f != null)
+        {
+          f = File.getById(dc, f.getId());
+          AnyToAny ata = AnyToAny.getNewOrExisting(dc, pc, "Configurationfile", f, true);
+          if (!ata.isInDatabase())
+          {
+            dc.saveItem(ata);
+          }
+          
+          getManualConfigureParameters();
+          Map<String, String> headers = getBaseFileHeaders(f);
+          configuration.setValue(serialFormatParameter.getName(), serialFormatParameter.getParameterType(), getBoolean(headers.get(serialFormatParameter.getName())));
+          configuration.setValue(versionNumberParameter.getName(), versionNumberParameter.getParameterType(), headers.get(versionNumberParameter.getName()));
+          configuration.setValue(execNameParameter.getName(), execNameParameter.getParameterType(), headers.get(execNameParameter.getName()));
+          configuration.setValue(geneAveragesParameter.getName(), geneAveragesParameter.getParameterType(), getBoolean(headers.get(geneAveragesParameter.getName())));
+          configuration.setValue(minChannelsParameter.getName(), minChannelsParameter.getParameterType(), new Integer(headers.get(minChannelsParameter.getName())));
+          configuration.setValue(maxChannelsParameter.getName(), maxChannelsParameter.getParameterType(), new Integer(headers.get(maxChannelsParameter.getName())));
+          configuration.setValue(leaveStdinParameter.getName(), leaveStdinParameter.getParameterType(), getBoolean(headers.get(leaveStdinParameter.getName())));
+          configuration.setValue(leaveStdoutParameter.getName(), leaveStdoutParameter.getParameterType(), getBoolean(headers.get(leaveStdoutParameter.getName())));
+          configuration.setValue(usedColumnsParameter.getName(), usedColumnsParameter.getParameterType(), headers.get(usedColumnsParameter.getName()));
+          configuration.setValue(usedFieldsParameter.getName(), usedFieldsParameter.getParameterType(), headers.get(usedFieldsParameter.getName()));
+          
+          response.setDone("Configured plug-in with file.");
+        }
+        else
+        {
+          response.setContinue(Base1PluginExecuter.COMMAND_MANUAL_CONFIG);
+        }
+      }
+      else if (command.equals(Base1PluginExecuter.COMMAND_MANUAL_CONFIG))
+      {
+        storeValue(configuration, request, serialFormatParameter);
+        storeValue(configuration, request, versionNumberParameter);
+        storeValue(configuration, request, execNameParameter);
+        storeValue(configuration, request, geneAveragesParameter);
+        storeValue(configuration, request, minChannelsParameter);
+        storeValue(configuration, request, maxChannelsParameter);
+        storeValue(configuration, request, leaveStdinParameter);
+        storeValue(configuration, request, leaveStdoutParameter);
+        storeValue(configuration, request, usedColumnsParameter);
+        storeValue(configuration, request, usedFieldsParameter);
+        
+        //TODO: Ask about parameters and create a config file
         response.setDone("Plugin configuration done.");
       }
       else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
       {
-        storeValue(job, request, bioAssaySetParameter);
-
+        storeValue(job, request, getSourceBioAssaySetParameter(null, null));
         for (PluginParameter<?> p : getJobParameters())
         {
           storeValue(job, request, p);
         }
-        
         response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
       }
+      else
+      {
+        throw new BaseException("Command unknown: "+command);
+      }
     }
     catch (Throwable ex)
     {
-      ex.printStackTrace();
       response.setError(ex.getMessage(), Arrays.asList(ex));
     }
-  }
-
+    finally
+    {
+      if (dc != null) 
+      {
+        dc.commit();
+        dc.close();
+      }
+    }
+  }
+  
+  
+  private void copy(File f, java.io.File d)
+    throws IOException
+  {
+    if (f != null && d.isDirectory())
+    {
+      java.io.File target = new java.io.File(d, f.getName());
+      InputStream in = f.getDownloadStream(0);
+      FileOutputStream out = new FileOutputStream(target);
+      byte[] buf = new byte[1024];
+      int i = 0;
+      while((i = in.read(buf)) != -1)
+      {
+        out.write(buf, 0, i);
+      }
+      in.close();
+      out.close();
+    }
+  }
+  
+  
+  private void createPluginDirectory()
+  {
+    DbControl dc = null;
+    try
+    {
+      dc = sc.newDbControl();
+      Directory parent = Directory.getByPath(dc, getPluginDirectoryPath().getParent());
+      if (Directory.exists(dc, parent, getPluginDirectoryPath().getDirectory(getPluginDirectoryPath().getDirectoryCount() - 1)))
+      {
+        int directoryId = Directory.getIdFromPath(dc, getPluginDirectoryPath());
+        RemovableUtil.removeRecursively(dc, Item.DIRECTORY, Collections.singleton(directoryId), true);
+        dc.commit();
+        dc = sc.newDbControl();
+      }
+      Directory d = Directory.getNew(dc, getPluginDirectoryPath());
+      dc.saveItem(d);
+      dc.commit();
+    }
+    finally
+    {
+      if (dc != null) dc.close(); 
+    }
+  }
+  
+
+  /**
+  */
+  @Override
+  public Collection<Permissions> getPermissions()
+  {
+    if (permissions.size() == 0)
+    {
+      permissions.add(new Permissions(Item.ANNOTATIONTYPE, null, EnumSet.of(Permission.READ)));
+      permissions.add(new Permissions(Item.DIRECTORY, null, EnumSet.of(Permission.CREATE, Permission.WRITE)));
+      permissions.add(new Permissions(Item.EXPERIMENT, null, EnumSet.of(Permission.WRITE)));
+      permissions.add(new Permissions(Item.FILE, EnumSet.of(Permission.USE), EnumSet.of(Permission.CREATE, Permission.WRITE)));
+      permissions.add(new Permissions(Item.PLUGINCONFIGURATION, EnumSet.of(Permission.WRITE), null));
+      permissions.add(new Permissions(Item.RAWBIOASSAY, null, EnumSet.of(Permission.READ)));
+    }
+    return permissions;
+  }
+  
   // ***
 
   // *** From Plugin interface
-  public MainType getMainType()
-  {
-    return MainType.ANALYZE;
-  }
 
   public About getAbout()
@@ -336 +404 @@
     return about;
   }
+  
 
   @Override
@@ -342 +411 @@
     return true;
   }
+  
 
   @Override
@@ -348 +418 @@
     return true;
   }
+  
 
   public void run(Request request, Response response, ProgressReporter progress)
@@ -354 +425 @@
     if (command.equals(Request.COMMAND_EXECUTE))
     {
+      DbControl dc = sc.newDbControl();
       try
       {
+        getManualConfigureParameters();
+        getConfigureJobParameters();
         progress.display(0, "Exporting data to be used by plugin.");
-        exportData();
-
+        createPluginDirectory();
+        File stdin = exportData(dc);
+        copy(stdin, getExecDirectory());
         progress.display(10, "Running on remote computation server.");
         
         String execPath = (String) configuration.getValue(execPathParameter.getName());
-        String execName = (String) configuration.getValue(execNameParameterName);
+        String execName = (String) configuration.getValue(execNameParameter.getName());
         Process p = Runtime.getRuntime().exec(execPath + java.io.File.separator + execName, null, getExecDirectory());
 
@@ -371 +446 @@
         StreamHandler inputStream = new StreamHandler(new BufferedInputStream(p.getInputStream()), new BufferedOutputStream(out));
         
-        java.io.File stdin = new java.io.File(getExecDirectory(), "stdin.txt");
-        
-        StreamHandler outputStream = new StreamHandler(
-          new BufferedInputStream(new FileInputStream(stdin)),
-          new BufferedOutputStream(p.getOutputStream()));
+        StreamHandler outputStream = new StreamHandler(new BufferedInputStream(stdin.getDownloadStream(0)), new BufferedOutputStream(p.getOutputStream()));
         
         inputStream.start();
@@ -383 +454 @@
         err.flush();
         out.close();
-
         
         int t;
@@ -394 +464 @@
         else
         {
-          DbControl dc = sc.newDbControl();
-  
-          BioAssaySet parentBas = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
-          parentBas = BioAssaySet.getById(dc, parentBas.getId());
+          BioAssaySet parentBas = getSourceBioAssaySet(dc);
           Transformation trans = parentBas.newTransformation(Job.getById(dc, job.getId()));
-          trans.setName("Something---");
+          trans.setName(getTransformationName(dc));
           dc.saveItem(trans);
           dc.commit();
@@ -414 +481 @@
       {
         getExecDirectory().delete();
+        dc.close();
       }
     }
@@ -421 +489 @@
     }
   }
-
-  // ***
-
-
-  private FlatFileParser getInitializedFlatFileParser(InputStream stream)
-    throws BaseException
-  {
-    FlatFileParser ffp = new FlatFileParser();
-    ffp.setSectionRegexp(Pattern.compile("section\\t(.*)"));
-    ffp.setHeaderRegexp(Pattern.compile("(.*?)\\s(.*)"));
-    ffp.setDataHeaderRegexp(Pattern.compile("%"));
-    ffp.setDataSplitterRegexp(Pattern.compile("\\t"));
-
-    ffp.setInputStream(stream, Config.getCharset());
-    return ffp;
-  }
-
-  private List<PluginParameter<?>> getConfigureParameters()
-  {
-    if (configureFileParameters == null)
-    {
-      configureFileParameters = new ArrayList<PluginParameter<?>>();
-
-      File f = (File) configuration.getValue(fileParameter.getName());
-      FlatFileParser ffp = getInitializedFlatFileParser(f.getDownloadStream(0));
-
-      try
-      {
-        FlatFileParser.LineType result = ffp.parseHeaders();
-        if (result != FlatFileParser.LineType.UNKNOWN)
-        {
-          if (!ffp.getLine(0).line().equals("BASEfile"))
-          {
-            throw new InvalidDataException(
-              "File '" + f + "' is not a valid basefile. First line (" + ffp.getLine(0).line() + ") must be BASEfile.");
-          }
-
-          FlatFileParser.Line section = ffp.nextSection();
-          while (section != null && !section.name().equals("plugin"))
-          {
-            section = ffp.nextSection();
-          }
-          if (section == null)
-          {
-            throw new InvalidDataException(
-              "File '" + f + "' is not a valid plugin configuration. cannt find the plugin section.");
-          }
-          ffp.parseHeaders();
-        }
-        else
-        {
-          throw new InvalidDataException("Unable to parse configuration file '" + f + "'.");
-        }
-      }
-      catch (IOException e)
-      {
-        throw new BaseException("Unable to read the configuration file: " + e.getMessage());
-      }
-      configureFileParameters.add(new PluginParameter<String>(
-        versionNumberParameterName,
+  
+
+  private File exportData(DbControl dc)
+  {
+    try
+    {
+      Directory d = Directory.getByPath(dc, getPluginDirectoryPath());
+      File file = File.getFile(dc, d, "stdin.txt", true);
+      file.setMimeTypeAuto("text/plain", null);
+      if(!file.isInDatabase()) dc.saveItem(file);
+      
+      BioAssaySet bas = getSourceBioAssaySet(dc);
+      
+      String usedColumns = (String) configuration.getValue(usedColumnsParameter.getName());
+      List<String> reporterFields = Arrays.asList(usedColumns.split("\\\\t"));
+      
+      String usedFields = (String) configuration.getValue(usedFieldsParameter.getName());
+      List<String> spotFields = Arrays.asList(usedFields.split("\\\\t"));
+      
+      Boolean mergeReporters = (Boolean) configuration.getValue(geneAveragesParameter.getName());
+      
+      Map<String, String> parameters = new HashMap<String, String>();
+      for (PluginParameter<?> pp : getJobParameters())
+      {
+        String name = pp.getName();
+        Object value = job.getValue(name);
+        parameters.put(name, value == null ? "" : value.toString());
+      }
+      
+      BioAssaySetExporter exporter = new BioAssaySetExporter();
+      if ((Boolean) configuration.getValue(serialFormatParameter.getName()))
+      {
+        exporter.exportBaseFileSerial(bas, file, parameters, reporterFields, spotFields, mergeReporters);
+      }
+      else
+      {
+        exporter.exportBaseFileMatrix(bas, file, parameters, reporterFields, spotFields, mergeReporters);
+      }
+      return file;
+    }
+    catch (IOException e)
+    {
+      throw new BaseException(e);
+    }
+    catch (SQLException e)
+    {
+      throw new BaseException(e);
+    } 
+  }
+  
+  
+  private List<AnnotationType> getAnnotationTypes(DbControl dc, Experiment e)
+  {
+    ItemQuery<AnnotationType> query = e.getExperimentalFactors();
+    query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+    query.order(Orders.asc(Hql.property("name")));
+    return query.list(dc);
+  }
+  
+  
+  
+  private Map<String, String> getBaseFileHeaders(File f)
+    throws IOException
+  {
+    FlatFileParser ffp = getInitializedFlatFileParser(f.getDownloadStream(0));
+    ffp.setMinDataColumns(8);
+
+    FlatFileParser.Line s = ffp.nextSection();
+    ffp.parseHeaders();
+    if (!s.name().equals("plugin"))
+    {
+      throw new BaseException("Bad format on configfile.");
+    }
+    
+    HashMap<String, String> headers = new HashMap<String, String>();
+    for (String header : ffp.getHeaderNames())
+    {
+      headers.put(header, ffp.getHeader(header));
+    }
+    return headers;
+  }
+  
+  
+  private Boolean getBoolean(String s)
+  {
+    return s.equals("0") ? false : true;
+  }
+  
+  private RequestInformation getManualConfigureParameters()
+  {
+    if (configureManual == null)
+    {
+      List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
+
+      versionNumberParameter = new PluginParameter<String>(
+        "versionNumber",
         "Version",
         "The version of this plug-in",
-        new StringParameterType(255, ffp.getHeader(versionNumberParameterName), true)));
-
-      configureFileParameters.add(new PluginParameter<String>(
-        execNameParameterName,
+        new StringParameterType(255, null, false));
+      parameters.add(versionNumberParameter);
+      
+      usedColumnsParameter = new PluginParameter<String>(
+        "usedColumns",
+        "Columns",
+        "A tab separeted sting of field namnes. A field is a value from the bioassay, the rawdata or feature",
+        new StringParameterType(null, null, true));
+      parameters.add(usedColumnsParameter);
+      
+      usedFieldsParameter = new PluginParameter<String>(
+        "usedFields",
+        "Fields",
+        "A tab separeted sting of field namnes. A field is a value from the bioassay or the rawdata",
+        new StringParameterType(null, null, true));
+      parameters.add(usedFieldsParameter);
+      
+      execNameParameter = new PluginParameter<String>(
+        "execName",
         "Name of executable",
         "The name of the file to be executed.",
-        new StringParameterType(255, ffp.getHeader(execNameParameterName), true)));
-
-      configureFileParameters.add(new PluginParameter<String>(
-        usedColumnsParameterName,
-        "Columns",
-        "A tab separeted sting of field namnes. A field is a value from the bioassay, the rawdata or feature",
-        new StringParameterType(null, ffp.getHeader(usedColumnsParameterName), true)));
-
-      configureFileParameters.add(new PluginParameter<String>(
-        usedFieldsParameterName,
-        "Fields",
-        "A tab separeted sting of field namnes. A field is a value from the bioassay or the rawdata",
-        new StringParameterType(null, ffp.getHeader(usedFieldsParameterName), true)));
-
-      configureFileParameters.add(new PluginParameter<Boolean>(
-        geneAveragesParameterName,
+        new StringParameterType(255, null, true));
+      parameters.add(execNameParameter);
+      
+      geneAveragesParameter = new PluginParameter<Boolean>(
+        "geneAverages",
         "Average on reporters",
         "Average on reporters within each assay",
-        new BooleanParameterType(new Boolean(ffp.getHeader(geneAveragesParameterName).equals("0") ? false : true), true)));
-
-      Enumeration<String, String> formatEnum = new Enumeration<String, String>();
-      formatEnum.add("0", "Normal BASEfile (one big matrix)");
-      formatEnum.add("1", "Serial BASEfile (one section per assay)");
-      configureFileParameters.add(new PluginParameter<String>(
-        serialFormatParameterName,
+        new BooleanParameterType(false, true));
+      parameters.add(geneAveragesParameter);
+
+      Enumeration<Boolean, String> format = new Enumeration<Boolean, String>();
+      format.add(false, "Normal BASEfile (one big matrix)");
+      format.add(true, "Serial BASEfile (one section per assay)");
+      serialFormatParameter = new PluginParameter<Boolean>(
+        "serialFormat",
         "Data format",
         "The format of the datafile can either be in a serial or matrix format",
-        new StringParameterType(1, ffp.getHeader(serialFormatParameterName), true, 1, 0, 0, formatEnum)));
-
-      configureFileParameters.add(new PluginParameter<Boolean>(
-        leaveStdinParameterName,
+        new BooleanParameterType(null, true, 1, format));
+      parameters.add(serialFormatParameter);
+      
+      leaveStdinParameter = new PluginParameter<Boolean>(
+        "leaveStdin",
         "Leave stdin.txt",
         "If the file stdin.txt should be removed after the plug-in execution or not",
-        new BooleanParameterType(new Boolean(ffp.getHeader(leaveStdinParameterName).equals("0") ? false : true), true)));
-
-      configureFileParameters.add(new PluginParameter<Boolean>(
-        leaveStdoutParameterName,
+        new BooleanParameterType(false, true));
+      parameters.add(leaveStdinParameter);
+      
+      leaveStdoutParameter = new PluginParameter<Boolean>(
+        "leaveStdout",
         "Leave stdout.txt",
         "If the file stdout.txt should be removed after the plug-in execution or not",
-        new BooleanParameterType(new Boolean(ffp.getHeader(leaveStdoutParameterName).equals("0") ? false : true), true)));
-
-      configureFileParameters.add(new PluginParameter<Integer>(
-        minChannelsParameterName,
+        new BooleanParameterType(false, true));
+      parameters.add(leaveStdoutParameter);
+      
+      minChannelsParameter = new PluginParameter<Integer>(
+        "minChannels",
         "Min channels",
         "Minimum number of channels",
-        new IntegerParameterType(1, null, new Integer(ffp.getHeader(minChannelsParameterName)), true)));
-
-      configureFileParameters.add(new PluginParameter<Integer>(
-        maxChannelsParameterName,
+        new IntegerParameterType(1, null, 2, true));
+      parameters.add(minChannelsParameter);
+      
+      maxChannelsParameter = new PluginParameter<Integer>(
+        "maxChannels",
         "Max channels",
         "Maximum number of channels. 0 for infinity",
-        new IntegerParameterType(0, null, new Integer(ffp.getHeader(maxChannelsParameterName)), true)));
-
-    }
-    return configureFileParameters;
-  }
-
-  private List<PluginParameter<?>> getJobParameters()
+        new IntegerParameterType(0, null, 0, true));
+      parameters.add(maxChannelsParameter);
+      
+      configureManual = new RequestInformation(
+        Base1PluginExecuter.COMMAND_MANUAL_CONFIG,
+        "Parse configuration file",
+        "These parameters are parsed from the configuration file",
+        parameters);
+    }
+
+    return configureManual;
+  }
+
+  
+  private RequestInformation getConfigureJobParameters()
     throws IOException
   {
-    if (jobParameters != null)
-    {
-      return jobParameters;
-    }
-    jobParameters = new ArrayList<PluginParameter<?>>();
-    File f = (File) configuration.getValue(fileParameter.getName());
-    if (f == null || f.isRemoved())
-    {
-      throw new BaseException(getAbout().getName() + " needs a configfile to execute.");
-    }
-    DbControl dc = sc.newDbControl();
-    BioAssaySet bas = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
-    if (bas == null)
-    {
-      int id = sc.getCurrentContext(Item.BIOASSAYSET).getId();
-      bas = BioAssaySet.getById(dc, id);
-    }
-    else
-    {
-      bas = BioAssaySet.getById(dc, bas.getId());
-    }
-    Experiment experiment = bas.getExperiment();
-    FlatFileParser ffp = getInitializedFlatFileParser(f.getDownloadStream(0));
-    ffp.setMinDataColumns(8);
-
-    FlatFileParser.Line section = ffp.nextSection();
-    while (section != null && !section.name().equals("plugin"))
-    {
-      section = ffp.nextSection();
-    }
-    ffp.parseHeaders();
-    List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
-    int valueTypeCol = columns.indexOf("valueType");
-    int nameCol = columns.indexOf("name");
-    int commonNameCol = columns.indexOf("commonName");
-    int optionsCol = columns.indexOf("options");
-    int defaultValueCol = columns.indexOf("defaultValue");
-    int enumOptionsCol = columns.indexOf("enumOptions");
-    int removedCol = columns.indexOf("removed");
-
-    while (ffp.hasMoreData())
-    {
-      FlatFileParser.Data dataline = ffp.nextData();
-      if (!Boolean.valueOf(dataline.get(removedCol)))
-      {
-        String name = dataline.get(nameCol);
-        String commonName = dataline.get(commonNameCol);
-        String options = dataline.get(optionsCol);
-        String defaultValue = dataline.get(defaultValueCol);
-        String enumOptions = dataline.get(enumOptionsCol);
-
-        PluginParameter<?> parameter = null;
-        switch (dataline.get(valueTypeCol).charAt(0))
-        {
-          // String parameter
-          case 't':
-          {
-            StringParameterType type = new StringParameterType(255, defaultValue, false, 1, new Integer(options), 1);
-            parameter = new PluginParameter<String>(name, commonName, "", type);
-            jobParameters.add(parameter);
-            break;
-          }
-          // Integer parameter
-          case 'i':
-          {
-            Integer defValue = defaultValue == null ? null : new Integer(defaultValue);
-            IntegerParameterType type = new IntegerParameterType(null, null, defValue, false, 1, new Integer(options), 1, null);
-            parameter = new PluginParameter<Integer>(name, commonName, "", type);
-            jobParameters.add(parameter);
-            break;
-          }
-          // HiddenString parameter
-          case 'h':
-          {
-            StringParameterType type = new StringParameterType(255, defaultValue, false, 1, 0, 1);
-            parameter = new PluginParameter<String>(name, commonName, "", type);
-            jobParameters.add(parameter);
-            break;
-          }
-          // Float parameter
-          case 'f':
-          {
-            Float defValue = defaultValue == null ? null : new Float(defaultValue);
-            FloatParameterType type = new FloatParameterType(null, null, defValue, false, 1, new Integer(options), 1, null);
-            parameter = new PluginParameter<Float>(name, commonName, "", type);
-            jobParameters.add(parameter);
-            break;
-          }
-          // TextField parameter
-          case 'a':
-          {
-            String[] wh = options.split(",");
-            StringParameterType type = new StringParameterType(
-              null,
-              defaultValue,
-              false,
-              1,
-              new Integer(wh[0]),
-              wh.length > 1 ? new Integer(wh[1]) : 1);
-            parameter = new PluginParameter<String>(name, commonName, "", type);
-            jobParameters.add(parameter);
-            break;
-          }
-          // Annotation parameter
-          case 'n':
-          {
-            List<AnnotationType> annotations = getAnnotationTypes(dc, bas);
-            if (!annotations.isEmpty())
-            {
-              Enumeration<String, String> enums = new Enumeration<String, String>();
-              for (AnnotationType at : annotations)
-              {
-                enums.add(at.getName(), at.getName());
-              }
-              StringParameterType type = new StringParameterType(255, defaultValue, true, 1, new Integer(options), 1, enums);
-              parameter = new PluginParameter<String>(name, commonName, "", type);
-              jobParameters.add(parameter);
-            }
-            break;
-          }
-          // Enum Parameter
-          case 'e':
-          {
-            Enumeration<String, String> enums = new Enumeration<String, String>();
-            String[] enumOptionsSplit = enumOptions.split("\\\\t");
-            for (int i = 0; i < enumOptionsSplit.length; i += 2)
-            {
-              enums.add(enumOptionsSplit[i], enumOptionsSplit[i + 1]);
-            }
-            StringParameterType type = new StringParameterType(255, defaultValue, true, 1, new Integer(options), 1, enums);
-            parameter = new PluginParameter<String>(name, commonName, "", type);
-            jobParameters.add(parameter);
-            break;
-          }
-        }
-      }
-    }
-
-    Directory homeDirectory = null;
-    try
-    {
-      homeDirectory = experiment.getDirectory();
-      if (!homeDirectory.hasPermission(Permission.WRITE)) homeDirectory = null;
-    }
-    catch (Throwable t)
-    {}
-    if (homeDirectory == null)
-    {
-      homeDirectory = User.getById(dc, sc.getLoggedInUserId()).getHomeDirectory();
-    }
-    if (homeDirectory == null)
-    {
-      homeDirectory = Directory.getById(dc, SystemItems.getId(Directory.ROOT));
-    }
-    sc.getLoggedInUserId();
-    jobParameters.add(new PluginParameter<String>(
-      "pluginDirectory",
-      "Plugin directory",
-      "The directory where a plugin can store its files.",
-      new PathParameterType(Path.Type.DIRECTORY, homeDirectory.getPath() + "/" + PluginConfiguration.getById(
-        dc,
-        configuration.getId()).getName(), true)));
-    dc.close();
-
-    return jobParameters;
-  }
-
+    if (configureJob == null)
+    {
+      // Parameters for CONFIGURE_JOB
+      List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
+      parameters.add(getSourceBioAssaySetParameter("Bioassay set", "The bioassay set that this plugin will run on"));
+      
+      parameters.addAll(getJobParameters());
+      configureJob = new RequestInformation(
+        Request.COMMAND_CONFIGURE_JOB,
+        "Configure job",
+        "Set the parameters needed for this plugin.",
+        parameters);
+    }
+    return configureJob;
+  }
+  
+  
   private RequestInformation getConfigurePluginParameters()
   {
@@ -733 +704 @@
   }
 
-  private RequestInformation getConfigureJobParameters()
+  
+  private java.io.File getExecDirectory()
+  {
+    if (execDirectory == null)
+    {
+      execDirectory = new java.io.File(
+        System.getProperty("java.io.tmpdir") + java.io.File.separator + about.getName() + java.io.File.separator + job.getId());
+      execDirectory.mkdirs();
+    }
+    return execDirectory;
+  }
+
+  
+  private FlatFileParser getInitializedFlatFileParser(InputStream stream)
+    throws BaseException
+  {
+    FlatFileParser ffp = new FlatFileParser();
+    ffp.setSectionRegexp(Pattern.compile("section\\t(.*)"));
+    ffp.setHeaderRegexp(Pattern.compile("(.*?)\\t(.*)"));
+    ffp.setDataHeaderRegexp(Pattern.compile("%"));
+    ffp.setDataSplitterRegexp(Pattern.compile("\\t"));
+
+    ffp.setInputStream(stream, Config.getCharset());
+    return ffp;
+  }
+  
+  
+  private List<PluginParameter<?>> getJobParameters()
     throws IOException
   {
-    if (configureJob == null)
-    {
-      // Parameters for CONFIGURE_JOB
-      List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
-      parameters.add(bioAssaySetParameter);
-      parameters.addAll(getJobParameters());
-      configureJob = new RequestInformation(
-        Request.COMMAND_CONFIGURE_JOB,
-        "Configure job",
-        "Set the parameters needed for this plugin.",
-        parameters);
-    }
-    return configureJob;
-  }
-
-  private RequestInformation getConfigureFileParameters()
-  {
-    if (configureFile == null)
-    {
-      // Parameters for PARSE_CONFIG_FILE
-
-      configureFile = new RequestInformation(
-        Base1PluginExecuter.PARSE_CONFIG_FILE,
-        "Parse configuration file",
-        "These parameters are parsed from the configuration file",
-        getConfigureParameters());
-    }
-
-    return configureFile;
-  }
-  
-  private void importFiles(int transformationId)
-  {
-    if (!(Boolean) configuration.getValue(leaveStdinParameterName))
-    {
-      deleteFile("stdin.txt");
-    }
-    if (!(Boolean) configuration.getValue(leaveStdoutParameterName))
-    {
-      deleteFile("stdout.txt");
-    }
-    DbControl dc = sc.newDbControl();
-    importTempFiles(dc, getExecDirectory().listFiles(), getPluginDirectory(dc));
-    dc.commit();
+    if (jobParameters != null)
+    {
+      return jobParameters;
+    }
+    jobParameters = new ArrayList<PluginParameter<?>>();  
+    DbControl dc = null;
     
-    
-    dc = sc.newDbControl();
-    Transformation t = Transformation.getById(dc, transformationId);
-    for(File f : getPluginDirectory(dc).getFiles().list(dc))
-    {
-      AnyToAny ata = AnyToAny.getNew(dc, t, f, f.getPath().toString(), false);
-      dc.saveItem(ata);
-    }
-    for(Directory d : getPluginDirectory(dc).getSubDirectories().list(dc))
-    {
-      AnyToAny ata = AnyToAny.getNew(dc, t, d, d.getPath().toString(), false);
-      dc.saveItem(ata);
-    }
-    dc.commit();
-  }
-
+    try
+    {
+      dc = sc.newDbControl();
+      AnyToAny ata = AnyToAny.getByName(dc, configuration.getPluginConfiguration(), "Configurationfile");
+      if (ata == null)
+      {
+        throw new BaseException("The plugin needs a configuration file to find the job parameters");
+      }
+      File f = File.getById(dc, ata.getTo().getId());
+      Experiment experiment = getCurrentBioAssaySet(dc).getExperiment();
+      FlatFileParser ffp = getInitializedFlatFileParser(f.getDownloadStream(0));
+      ffp.setMinDataColumns(8);
+      FlatFileParser.Line section = ffp.nextSection();
+      while (section != null && !section.name().equals("plugin"))
+      {
+        section = ffp.nextSection();
+      }
+      ffp.parseHeaders();
+      List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
+      int valueTypeCol = columns.indexOf("valueType");
+      int nameCol = columns.indexOf("name");
+      int commonNameCol = columns.indexOf("commonName");
+      int optionsCol = columns.indexOf("options");
+      int defaultValueCol = columns.indexOf("defaultValue");
+      int enumOptionsCol = columns.indexOf("enumOptions");
+      int removedCol = columns.indexOf("removed");
+      while (ffp.hasMoreData())
+      {
+        FlatFileParser.Data dataline = ffp.nextData();
+        if (!Boolean.valueOf(dataline.get(removedCol)))
+        {
+          String name = dataline.get(nameCol);
+          String commonName = dataline.get(commonNameCol);
+          String options = dataline.get(optionsCol);
+          String defaultValue = dataline.get(defaultValueCol);
+          String enumOptions = dataline.get(enumOptionsCol);
+
+          PluginParameter<?> parameter = null;
+          switch (dataline.get(valueTypeCol).charAt(0))
+          {
+            // String parameter
+            case 't':
+            {
+              StringParameterType type = new StringParameterType(255, defaultValue, false, 1, new Integer(options), 1);
+              parameter = new PluginParameter<String>(name, commonName, "", type);
+              jobParameters.add(parameter);
+              break;
+            }
+              // Integer parameter
+            case 'i':
+            {
+              Integer defValue = defaultValue == null ? null : new Integer(defaultValue);
+              IntegerParameterType type = new IntegerParameterType(null, null, defValue, false, 1, new Integer(options), 1, null);
+              parameter = new PluginParameter<Integer>(name, commonName, "", type);
+              jobParameters.add(parameter);
+              break;
+            }
+              // HiddenString parameter
+            case 'h':
+            {
+              StringParameterType type = new StringParameterType(255, defaultValue, false, 1, 0, 1);
+              parameter = new PluginParameter<String>(name, null, "", type);
+              jobParameters.add(parameter);
+              break;
+            }
+              // Float parameter
+            case 'f':
+            {
+              Float defValue = defaultValue == null ? null : new Float(defaultValue);
+              FloatParameterType type = new FloatParameterType(null, null, defValue, false, 1, new Integer(options), 1, null);
+              parameter = new PluginParameter<Float>(name, commonName, "", type);
+              jobParameters.add(parameter);
+              break;
+            }
+              // TextField parameter
+            case 'a':
+            {
+              String[] wh = options.split(",");
+              StringParameterType type = new StringParameterType(
+                null,
+                defaultValue,
+                false,
+                1,
+                new Integer(wh[0]),
+                wh.length > 1 ? new Integer(wh[1]) : 1);
+              parameter = new PluginParameter<String>(name, commonName, "", type);
+              jobParameters.add(parameter);
+              break;
+            }
+              // Annotation parameter
+            case 'n':
+            {
+              List<AnnotationType> annotations = getAnnotationTypes(dc, experiment);
+              if (!annotations.isEmpty())
+              {
+                Enumeration<String, String> enums = new Enumeration<String, String>();
+                for (AnnotationType at : annotations)
+                {
+                  enums.add(at.getName(), at.getName());
+                }
+                StringParameterType type = new StringParameterType(255, defaultValue, true, 1, new Integer(options), 1, enums);
+                parameter = new PluginParameter<String>(name, commonName, "", type);
+                jobParameters.add(parameter);
+              }
+              break;
+            }
+              // Enum Parameter
+            case 'e':
+            {
+              Enumeration<String, String> enums = new Enumeration<String, String>();
+              String[] enumOptionsSplit = enumOptions.split("\\\\t");
+              for (int i = 0; i < enumOptionsSplit.length; i += 2)
+              {
+                enums.add(enumOptionsSplit[i], enumOptionsSplit[i + 1]);
+              }
+              StringParameterType type = new StringParameterType(255, defaultValue, true, 1, new Integer(options), 1, enums);
+              parameter = new PluginParameter<String>(name, commonName, "", type);
+              jobParameters.add(parameter);
+              break;
+            }
+          }
+        }
+      }
+      String homeDirectoryPath = "";
+      Directory homeDirectory = experiment.getDirectory();
+      if (homeDirectory == null)
+      {
+        homeDirectoryPath = homeDirectory.getPath() + "/" + PluginConfiguration.getById(dc, configuration.getId()).getName();
+      }
+      pluginDirectoryParameter = new PluginParameter<String>(
+        "pluginDirectory",
+        "Plugin directory",
+        "The directory where a plugin can store its files.",
+        new PathParameterType(Path.Type.DIRECTORY, homeDirectoryPath, true));
+      jobParameters.add(pluginDirectoryParameter);
+    }
+    finally
+    {
+      dc.close();
+    }   
+
+    return jobParameters;
+  }
+  
+
+  private Path getPluginDirectoryPath()
+  {
+    Path p = new Path((String) job.getValue(pluginDirectoryParameter.getName()) + "/" + job.getId(), Path.Type.DIRECTORY);
+    return p;
+  }
+  
+  
   private int importData()
     throws IOException
@@ -804 +900 @@
 
     Job jobitem = Job.getById(dc, job.getId());
-    BioAssaySet parentBas = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
-    parentBas = BioAssaySet.getById(dc, parentBas.getId());
+    BioAssaySet parentBas = getSourceBioAssaySet(dc);
     Transformation t = parentBas.newTransformation(jobitem);
-    t.setName("Something---");
+    t.setName(getTransformationName(dc));
     dc.saveItem(t);
     
     BioAssaySet bas = null;
     SpotBatcher spotBatcher = null;
-//    PositionBatcher posBatcher = null;
 
     HashMap<String, BioAssay> idMap = new HashMap<String, BioAssay>();
@@ -827 +921 @@
       {
         bas = t.newProduct("new", "new", false);
-        bas.setName("Something after");
-//        dc.saveItem(bas);
+        bas.setName(getSourceBioAssaySet(dc).getName());
 
         List<String> columns = Arrays.asList(ffp.getHeader("columns").split("\\t"));
@@ -866 +959 @@
           BioAssay ba = bas.newBioAssay(baParents);
           ba.setName(name);
-//          dc.saveItem(ba);
           idMap.put(id, ba);
           dataline = ffp.nextData();
@@ -882 +974 @@
           bas = t.newProduct(null, "new", false);
           bas.setName("Something after");
-//          dc.saveItem(bas);
-        }
-        else
-        {
-//          posBatcher = bas.getPositionBatcher();
         }
         spotBatcher = bas.getSpotBatcher();
@@ -898 +985 @@
               BioAssay parent = BioAssay.getById(dc, Integer.parseInt(assayId));
               BioAssay ba = bas.newBioAssay(parent);
-//              dc.saveItem(ba);
               idMap.put(assayId, ba);
             }
@@ -1045 +1131 @@
                   {}
                 }
-//                if (posBatcher != null)
-//                {
-//                  if (reporter != null)
-//                  {
-//                    posBatcher.insert(position, Reporter.getById(dc, reporter));
-//                  }
-//                  else
-//                  {
-//                    posBatcher.insert(position, null);
-//                  }
-//                }
               }
               index += assayFields.size();
@@ -1077 +1152 @@
     return t.getId();
   }
-
-  private void exportData()
-    throws IOException, SQLException
-  {
-    if ((Boolean) configuration.getValue(geneAveragesParameterName))
-    {
-      throw new BaseException(geneAveragesParameterName + " isnt implemented yet.");
-    }
-    DbControl dc = sc.newDbControl();
-    PrintWriter out = new PrintWriter(new java.io.File(getExecDirectory(), "stdin.txt"));
-    BioAssaySet bas = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
-    bas = BioAssaySet.getById(dc, bas.getId());
-    getBase1Columns();
-
-    // Print parameters
-    out.println("BASEfile");
-    for (PluginParameter<?> p : getJobParameters())
-    {
-      Object value = job.getValue(p.getName()) == null ? "" : job.getValue(p.getName());
-      out.println(p.getName() + "\t" + value);
-    }
-    out.println("pluginVersion\t" + job.getValue(versionNumberParameterName));
-    out.println("%");
-    out.println();
-
-    // Print assays
-    // Collect annotations
-    List<AnnotationType> annotations = getAnnotationTypes(dc, bas);
-    String annotationString = "";
-    for (AnnotationType at : annotations)
-    {
-      annotationString += "\t" + at.getName();
-    }
-    out.println("section\tassays");
-    out.println("count\t" + bas.getBioAssays().count(dc));
-    out.println("columns\tid\tname" + annotationString);
-    out.println("annotationColumns" + annotationString);
-    out.println("%");
-    for (BioAssay ba : bas.getBioAssays().list(dc))
-    {
-      out.print(ba.getId() + "\t" + ba.getName());
-      for (AnnotationType at : annotations)
-      {
-        out.print("\t");
-        BioAssaySetUtil.getAnnotationValues(dc, ba, at);
-        Set<?> v = BioAssaySetUtil.getAnnotationValues(dc, ba, at);
-        if (!v.isEmpty())
-        {
-          out.print(v.iterator().next());
-        }
-      }
-      out.println();
-    }
-    out.println();
-
-    // Print spots
-    List<String> columns = new ArrayList<String>(
-      Arrays.asList(((String) configuration.getValue(usedColumnsParameterName)).split("\\\\t")));
-    List<String> fields = new ArrayList<String>(
-      Arrays.asList(((String) configuration.getValue(usedFieldsParameterName)).split("\\\\t")));
-    columns.retainAll(base1columns.keySet());
-    fields.retainAll(base1columns.keySet());
-    
-    String fieldString = fields.toString().substring(1, fields.toString().length() - 1).replace(", ", "\t");
-    String columnString = columns.toString().substring(1, columns.toString().length() - 1).replace(", ", "\t") + "\tassayData";
-    String spotHeader = "section\tspots" + "\nchannels\t" + bas.getRawDataType().getChannels() + "\nassayFields\t" + fieldString + "\ncolumns\t" + columnString;
-    if (configuration.getValue(serialFormatParameterName).equals("1"))
-    {
-      for (BioAssay ba : bas.getBioAssays().list(dc))
-      {
-        out.println(spotHeader);
-        out.println("assays\t" + ba.getId());
-        out.println("count\t" + ba.getNumSpots());
-        out.println("%");
-
-        List<Integer> columnIndex = new ArrayList<Integer>(columns.size());
-        List<Integer> fieldIndex = new ArrayList<Integer>(fields.size());
-        DynamicSpotQuery q = createSpotQuery(ba.getSpotData(), columns, fields);
-        DynamicResultIterator result = q.iterate(dc);
-        
-        for (String column : columns)
-        {
-          columnIndex.add(result.getIndex(column));
-        }
-        for (String field : fields)
-        {
-          fieldIndex.add(result.getIndex(field));
-        }
-
-        while (result.hasNext())
-        {
-          SqlResult r = result.next();
-          boolean del = false;
-          for (Integer column : columnIndex)
-          {
-            if (del)
-            {
-              out.print("\t");
-            }
-            out.print(r.getString(column) != null ? r.getString(column) : "");
-            del = true;
-          }
-          for (Integer field : fieldIndex)
-          {
-            out.print("\t");
-            out.print(r.getString(field) != null ? r.getString(field) : "");
-          }
-          out.print("\n");
-        }
-        out.println();
-      }
-    }
-    else
-    {
-      ItemQuery<BioAssay> assayQuery = bas.getBioAssays();
-      assayQuery.order(Orders.asc(Hql.property("dataCubeColumn.columnNo")));
-      
-      ArrayList<Short> columnNo = new ArrayList<Short>((int) assayQuery.count(dc));
-      
-      out.println(spotHeader);
-      out.print("assays");
-      for (BioAssay ba : assayQuery.list(dc))
-      {
-        out.print("\t" + ba.getId());
-        columnNo.add(ba.getDataCubeColumnNo());
-      }
-      out.println("\ncount\t" + bas.getNumSpots());
-      out.print("%");
-
-      List<Integer> columnIndex = new ArrayList<Integer>(columns.size());
-      List<Integer> fieldIndex = new ArrayList<Integer>(fields.size());
-      DynamicSpotQuery q = createSpotQuery(bas.getSpotData(), columns, fields);
-      q.select(Selects.expression(Dynamic.column(VirtualColumn.COLUMN), "column"));
-      q.order(Orders.asc(Dynamic.column(VirtualColumn.POSITION)));
-      q.order(Orders.asc(Dynamic.column(VirtualColumn.COLUMN)));
-      DynamicResultIterator result = q.iterate(dc);
-      
-
-      for (String column : columns)
-      {
-        columnIndex.add(result.getIndex(column));
-      }
-      for (String field : fields)
-      {
-        fieldIndex.add(result.getIndex(field));
-      }
-      int columnNoIndex = result.getIndex("column");
-      int positionIndex = result.getIndex("position");
-      
-      
-      int i = Integer.MAX_VALUE;
-      int prevPos = Integer.MAX_VALUE;
-      while (result.hasNext())
-      {
-        SqlResult r = result.next();
-        
-        if (prevPos != r.getInt(positionIndex) || i > columnNo.size())
-        {
-          if (i < columnNo.size())
-          {
-            out.print(getString(getString("\t", fieldIndex.size()), columnNo.size() - i));
-          }
-          i = 0;
-          out.println();
-        }
-        
-        if (i == 0)
-        {
-          boolean del = false;
-          for (Integer column : columnIndex)
-          {
-            if (del)
-            {
-              out.print("\t");
-            }
-            out.print(r.getString(column) != null ? r.getString(column) : "");
-            del = true;
-          }
-        }
-        
-        while (i < columnNo.size() && columnNo.get(i) != r.getShort(columnNoIndex))
-        {
-          out.print(getString("\t", fieldIndex.size()));
-          i++;
-        }
-
-        for (Integer field : fieldIndex)
-        {
-          out.print("\t");
-          out.print(r.getString(field) != null ? r.getString(field) : "");
-        }
-        i++;
-        
-        prevPos = r.getInt(positionIndex);
-      }
-    }
-    out.close();
-    dc.close();
-  }
-
-  private Map<String, Select> getBase1Columns()
-  {
-    if (base1columns == null)
-    {
-      base1columns = new HashMap<String, Select>();
-
-      // Reporter fields
-      base1columns.put("accession", Selects.expression(Dynamic.reporter("accession"), "accession"));
-      base1columns.put("antibiotics", Selects.expression(Dynamic.reporter("antibiotics"), "antibiotics"));
-      base1columns.put("chromosome", Selects.expression(Dynamic.reporter("chromosome"), "chromosome"));
-      base1columns.put("clusterId", Selects.expression(Dynamic.reporter("clusterId"), "clusterId"));
-      base1columns.put("cytoBand", Selects.expression(Dynamic.reporter("cytoband"), "cytoBand"));
-      base1columns.put("length", Selects.expression(Dynamic.reporter("length"), "length"));
-      base1columns.put("library", Selects.expression(Dynamic.reporter("library"), "library"));
-      base1columns.put("locusLink", Selects.expression(Dynamic.reporter("locusLink"), "locusLink"));
-      base1columns.put("markers", Selects.expression(Dynamic.reporter("markers"), "markers"));
-      base1columns.put("nid", Selects.expression(Dynamic.reporter("nid"), "nid"));
-      base1columns.put("omim", Selects.expression(Dynamic.reporter("omim"), "omim"));
-      base1columns.put("reporter", Selects.expression(Dynamic.reporter("id"), "reporter"));
-      base1columns.put("reporterId", Selects.expression(Dynamic.reporter("externalId"), "reporterId"));
-      base1columns.put("sequence", Selects.expression(Dynamic.reporter("sequence"), "sequence"));
-      base1columns.put("species", Selects.expression(Dynamic.reporter("species"), "species"));
-      base1columns.put("tissue", Selects.expression(Dynamic.reporter("tissue"), "tissue"));
-      base1columns.put("vector", Selects.expression(Dynamic.reporter("vector"), "vector"));
-
-      // Spot fields
-      base1columns.put("position", Selects.expression(Dynamic.column(VirtualColumn.POSITION), "position"));
-      base1columns.put("intensity1", Selects.expression(Dynamic.column(VirtualColumn.channel(1)), "intensity1"));
-      base1columns.put("intensity2", Selects.expression(Dynamic.column(VirtualColumn.channel(2)), "intensity2"));
-      base1columns.put("l10intgmean1_2", Selects.expression(Expressions.log10(Expressions.sqrt(Expressions.multiply(
-        Dynamic.column(VirtualColumn.channel(1)),
-        Dynamic.column(VirtualColumn.channel(2))))), "l10intgmean1_2"));
-      base1columns.put("l2intsum1_2", Selects.expression(Expressions.log2(Expressions.sqrt(Expressions.add(
-        Dynamic.column(VirtualColumn.channel(1)),
-        Dynamic.column(VirtualColumn.channel(2))))), "l2intsum1_2"));
-      base1columns.put("l2ratio1_2", Selects.expression(Expressions.log2(Expressions.divide(
-        Dynamic.column(VirtualColumn.channel(1)),
-        Dynamic.column(VirtualColumn.channel(2)))), "l2ratio1_2"));
-      base1columns.put("maxint1_2", Selects.expression(Expressions.caseWhen(
-        Dynamic.column(VirtualColumn.channel(1)),
-        new WhenStatement(
-          Restrictions.lt(Dynamic.column(VirtualColumn.channel(1)), Dynamic.column(VirtualColumn.channel(2))),
-          Dynamic.column(VirtualColumn.channel(2)))), "maxint1_2"));
-      base1columns.put("minint1_2", Selects.expression(Expressions.caseWhen(
-        Dynamic.column(VirtualColumn.channel(1)),
-        new WhenStatement(
-          Restrictions.gt(Dynamic.column(VirtualColumn.channel(1)), Dynamic.column(VirtualColumn.channel(2))),
-          Dynamic.column(VirtualColumn.channel(2)))), "minint1_2"));
-      base1columns.put("ratio1_2", Selects.expression(Expressions.divide(
-        Dynamic.column(VirtualColumn.channel(1)),
-        Dynamic.column(VirtualColumn.channel(2))), "ratio1_2"));
-
-      // Rawdata fields
-      base1columns.put("BCh1Mean", Selects.expression(Dynamic.rawData("ch1BgMean"), "BCh1Mean"));
-      base1columns.put("BCh1Median", Selects.expression(Dynamic.rawData("ch1BgMedian"), "BCh1Median"));
-      base1columns.put("BCh1SD", Selects.expression(Dynamic.rawData("ch1BgSd"), "BCh1SD"));
-      base1columns.put("BCh2Mean", Selects.expression(Dynamic.rawData("ch2BgMean"), "BCh2Mean"));
-      base1columns.put("BCh2Median", Selects.expression(Dynamic.rawData("ch2BgMedian"), "BCh2Median"));
-      base1columns.put("BCh2SD", Selects.expression(Dynamic.rawData("ch2BgSd"), "BCh2SD"));
-      base1columns.put("block", Selects.expression(Dynamic.rawData("block"), "block"));
-      base1columns.put("BPixels", Selects.expression(Dynamic.rawData("bgPixels"), "BPixels"));
-      base1columns.put("CV", Selects.expression(Dynamic.rawData("CV"), "CV"));
-      base1columns.put("dia", Selects.expression(Dynamic.rawData("diameter"), "dia"));
-      base1columns.put("FCh1Mean", Selects.expression(Dynamic.rawData("ch1FgMean"), "FCh1Mean"));
-      base1columns.put("FCh1Median", Selects.expression(Dynamic.rawData("ch1FgMedian"), "FCh1Mean"));
-      base1columns.put("FCh1SD", Selects.expression(Dynamic.rawData("ch1FgSd"), "FCh1SD"));
-      base1columns.put("FCh2Mean", Selects.expression(Dynamic.rawData("ch2FgMean"), "FCh2Mean"));
-      base1columns.put("FCh2Median", Selects.expression(Dynamic.rawData("ch2FgMedian"), "FCh2Median"));
-      base1columns.put("FCh2SD", Selects.expression(Dynamic.rawData("ch2FgSd"), "FCh2SD"));
-      base1columns.put("flags", Selects.expression(Dynamic.rawData("flags"), "flags"));
-      base1columns.put("FPixels", Selects.expression(Dynamic.rawData("fgPixels"), "FPixels"));
-      base1columns.put("MValue", Selects.expression(Dynamic.rawData("mValue"), "MValue"));
-      base1columns.put("percCh1Sat", Selects.expression(Dynamic.rawData("ch1PercSat"), "percCh1Sat"));
-      base1columns.put("percCh1SD1", Selects.expression(Dynamic.rawData("ch1PercSD1"), "percCh1SD1"));
-      base1columns.put("percCh1SD2", Selects.expression(Dynamic.rawData("ch1PercSD2"), "percCh1SD1"));
-      base1columns.put("percCh2Sat", Selects.expression(Dynamic.rawData("ch2PercSat"), "percCh2Sat"));
-      base1columns.put("percCh2SD1", Selects.expression(Dynamic.rawData("ch2PercSD1"), "percCh2SD1"));
-      base1columns.put("percCh2SD2", Selects.expression(Dynamic.rawData("ch2PercSD2"), "percCh2SD2"));
-      base1columns.put("ratiosSD", Selects.expression(Dynamic.rawData("ratiosSd"), "ratiosSD"));
-      base1columns.put("rgnR2", Selects.expression(Dynamic.rawData("rgnR2"), "rgnR2"));
-      base1columns.put("rgnRatio", Selects.expression(Dynamic.rawData("rgnRatio"), "rgnRatio"));
-      base1columns.put("numCol", Selects.expression(Dynamic.rawData("metaGridX"), "numCol"));
-      base1columns.put("numRow", Selects.expression(Dynamic.rawData("metaGridY"), "numRow"));
-      base1columns.put("x", Selects.expression(Dynamic.rawData("x"), "x"));
-      base1columns.put("y", Selects.expression(Dynamic.rawData("y"), "y"));
-      base1columns.put("rawPosition", Selects.expression(Dynamic.rawData("position"), "rawPosition"));
-
-      base1columns.put("SNRCh1Mean", Selects.expression(
-        Expressions.divide(Expressions.subtract(
-          Expressions.selected(Dynamic.selectRawData("ch1FgMean")),
-          Expressions.selected(Dynamic.selectRawData("ch1BgMean"))), Expressions.selected(Dynamic.selectRawData("ch1BgSd"))),
-        "SNRCh1Mean"));
-      base1columns.put("SNRCh1Median", Selects.expression(
-        Expressions.divide(Expressions.subtract(
-          Expressions.selected(Dynamic.selectRawData("ch1FgMedian")),
-          Expressions.selected(Dynamic.selectRawData("ch1BgMedian"))), Expressions.selected(Dynamic.selectRawData("ch1BgSd"))),
-        "SNRCh1Median"));
-      base1columns.put("SNRCh2Mean", Selects.expression(
-        Expressions.divide(Expressions.subtract(
-          Expressions.selected(Dynamic.selectRawData("ch2FgMean")),
-          Expressions.selected(Dynamic.selectRawData("ch2BgMean"))), Expressions.selected(Dynamic.selectRawData("ch2BgSd"))),
-        "SNRCh2Mean"));
-      base1columns.put("SNRCh2Median", Selects.expression(
-        Expressions.divide(Expressions.subtract(
-          Expressions.selected(Dynamic.selectRawData("ch2FgMedian")),
-          Expressions.selected(Dynamic.selectRawData("ch2BgMedian"))), Expressions.selected(Dynamic.selectRawData("ch2BgSd"))),
-        "SNRCh2Median"));
-
-      /*
-       * CCh1Mean CCh1Median CCh2Mean CCh2Median MeanRatio MedianRatio
-       */
-
-    }
-    return base1columns;
-
-  }
-
-  private DynamicSpotQuery createSpotQuery(DynamicSpotQuery query, List<String> columns, List<String> fields)
-  {
-    query.joinRawData(JoinType.LEFT);
-    query.joinReporters(JoinType.LEFT);
-    for (String s : columns)
-    {
-      Select select = base1columns.get(s);
-      query.select(select);
-    }
-
-    for (String s : fields)
-    {
-      Select select = base1columns.get(s);
-      query.select(select);
-    }
-
-    return query;
-  }
-
-  private java.io.File getExecDirectory()
-  {
-    if (execDirectory == null)
-    {
-      execDirectory = new java.io.File(
-        System.getProperty("java.io.tmpdir") + java.io.File.separator + about.getName() + java.io.File.separator + job.getId());
-      execDirectory.mkdirs();
-    }
-    return execDirectory;
-  }
+  
+
+  private void importFiles(int transformationId)
+  {
+    DbControl dc = null;
+    try
+    {
+      dc = sc.newDbControl();
+      Directory homeDirectory = Directory.getByPath(dc, getPluginDirectoryPath());
+      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();
+    }
+    finally
+    {
+      if (dc != null)
+      {
+        dc.close();
+      }
+    }
+  }
+
 
   private void importTempFiles(DbControl dc, java.io.File[] files, Directory d)
@@ -1456 +1221 @@
     }
   }
-
-  private Directory getPluginDirectory(DbControl dc)
-  {
-    if (pluginDirectory == null)
-    {
-      Path p = new Path((String) job.getValue(pluginDirectoryParameterName) + "/" + job.getId(), Path.Type.DIRECTORY);
-      try
-      {
-        int id = Directory.getIdFromPath(dc, p);
-        pluginDirectory = Directory.getById(dc, id);
-      }
-      catch (ItemNotFoundException e)
-      {
-        pluginDirectory = Directory.getNew(dc, p);
-        dc.saveItem(pluginDirectory);
-      }
-    }
-    return pluginDirectory;
-  }
-
-  public List<AnnotationType> getAnnotationTypes(DbControl dc, BioAssaySet bas)
-  {
-    ItemQuery<AnnotationType> query = bas.getExperiment().getExperimentalFactors();
-    query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
-    query.order(Orders.asc(Hql.property("name")));
-    return query.list(dc);
-  }
-
-  private void deleteFile(String name)
-  {
-    java.io.File file = new java.io.File(getExecDirectory(), name);
-    if (file.exists())
-    {
-      file.delete();
-    }
-  }
-  
-  private String getString(String s, int n)
-  {
-    StringBuffer sb = new StringBuffer(s.length() * n);
-    for (int i = 0; i < n; i++)
-    {
-      sb.append(s);
-    }
-    return sb.toString();
-  }
     
   
@@ -1536 +1255 @@
   }
 
+
   private class PosRep
   {
@@ -1572 +1292 @@
       return false;
     }
-
+    
     @Override
     public int hashCode()
@@ -1578 +1298 @@
       return getPosition();
     }
-    
-    
   }
 }