Changeset 4537

Timestamp:

Sep 18, 2008, 11:23:28 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 2.8.2 to the trunk

Location:

trunk

Files:

• build.xml (modified) (1 diff)
• credits.txt (modified) (1 diff)
• doc/src/docbook/admindoc/extensions.xml (modified) (1 diff)
• doc/src/docbook/admindoc/installation_upgrade.xml (modified) (3 diffs)
• doc/src/docbook/admindoc/plugin_installation.xml (modified) (1 diff)
• doc/src/docbook/developerdoc/api_overview.xml (modified) (3 diffs)
• doc/src/docbook/developerdoc/base_overview.xml (modified) (1 diff)
• doc/src/docbook/developerdoc/core_ref.xml (modified) (9 diffs)
• doc/src/docbook/faq/faqs.xml (modified) (1 diff)
• doc/src/docbook/overviewdoc/resources.xml (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (4 diffs)
• src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (1 diff)
• src/test/Base1NullPlugin.java (modified) (1 diff)
• src/test/TestAnalyzePluginUtil.java (modified) (5 diffs)
• src/test/TestBase1PluginExecuter.java (modified) (6 diffs)
• src/test/TestBioAsssaySetExporter.java (modified) (1 diff)
• src/test/TestExperiment.java (modified) (10 diffs)
• src/test/TestLowessNormalization.java (modified) (1 diff)
• src/test/TestMedianRatioNormalization.java (modified) (1 diff)
• src/test/data/test.nullplugin.base (modified) (1 diff)
• src/test/data/test.nullplugin.matrix.base (copied) (copied from tags/2.8.2/src/test/data/test.nullplugin.matrix.base)
• www (modified) (1 prop)
• www/admin/plugindefinitions/select_installation_type.jsp (modified) (1 diff)
• www/admin/softwaretypes/view_softwaretype.jsp (modified) (1 diff)
• www/biomaterials/samples/list_samples.jsp (modified) (1 diff)
• www/common/columns/confirm_delete.jsp (modified) (1 diff)
• www/common/columns/save_preset.jsp (modified) (1 diff)
• www/common/context/saveas.jsp (modified) (1 diff)
• www/common/import/no_fileformat.jsp (modified) (1 diff)
• www/common/import/select_plugin.jsp (modified) (1 diff)
• www/common/plugin/finish_job.jsp (modified) (1 diff)
• www/common/plugin/select_plugin.jsp (modified) (1 diff)
• www/extensions (copied) (copied from tags/2.8.2/www/extensions)
• www/extensions/readme.txt (copied) (copied from tags/2.8.2/www/extensions/readme.txt)
• www/logout.jsp (modified) (1 diff)
• www/plugins/net/sf/basedb/clients/web/plugins/simple_export.jsp (modified) (1 diff)
• www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp (modified) (1 diff)
• www/plugins/net/sf/basedb/plugins/jep_filter.jsp (modified) (1 diff)
• www/plugins/net/sf/basedb/plugins/jep_intensity_transformer.jsp (modified) (1 diff)
• www/views/experiments/overview/save_preset.jsp (modified) (1 diff)

trunk/build.xml

@@ -1405 +1405 @@
       <!--fileset dir="doc" includes="development/**/*" /-->
       <fileset dir="doc" includes="licenses/**/*" />
-      <fileset dir="doc" includes="specifications/**/*" />
+      <fileset dir="doc" includes="historical/admin/**/*" />
+      <fileset dir="doc" includes="historical/development/**/*" />
+      <fileset dir="doc" includes="historical/specifications/**/*" />
       <!--fileset dir="doc" includes="user/**/*" /-->
       <fileset dir="doc" includes="*.*" />

trunk/credits.txt

@@ -26 +26 @@
 USA.
 
-The current BASE team is (at BASE 2.8.1 release)
+The current BASE team is (at BASE 2.8.2 release)
 
 Jari Häkkinen

trunk/doc/src/docbook/admindoc/extensions.xml

@@ -65 +65 @@
       folder. This is the only place were extensions can be installed.
     </para>
+    
+    <note>
+      <title>Make sure the extensions folder is writable by Tomcat</title>
+      <para>
+        The extension you are installing may include resources such as HTML
+        files, JSP scripts, images, etc. that needs to be extracted to the 
+        web application path before they can be used. This extraction is
+        automatically done by the extensions system, but you have to make
+        sure that the user account Tomcat is running as has permission
+        to create (and delete) new files in the 
+        <filename class="directory">&lt;base-dir&gt;/www/extensions</filename>
+        directory.
+      </para>
+    </note>
     
     <para>

trunk/doc/src/docbook/admindoc/installation_upgrade.xml

@@ -833 +833 @@
               is available in the
               <ulink
-              url="http://base.thep.lu.se/chrome/site/doc/development/build.html">building
+              url="http://base.thep.lu.se/chrome/site/doc/historical/development/build.html">building
               BASE document</ulink>. When you return back after
               compiling in the subversion tree you can follow the
@@ -976 +976 @@
             There is an
             administrator <ulink
-            url="http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html">document
+            url="http://base.thep.lu.se/chrome/site/doc/historical/admin/extended-properties.html">document
             discussing extended properties</ulink> available. If you
             plan to perform a migration of a BASE version 1.2 database you
@@ -1027 +1027 @@
 <programlisting>cd /path/to/tomcat/webapps
 ln -s /path_to_base/www base2</programlisting>
+          </para>
+          <para>
+            If you plan to install extensions you should make sure that
+            the <filename class="directory">&lt;base-dir&gt;/www/extensions</filename>
+            directory is writable by the user account Tomcat is running as.
+          </para>
+          <para>
             Start/restart Tomcat, and try http://hostname:8080/base2
             (change <emphasis>hostname</emphasis> to your hostname) in

trunk/doc/src/docbook/admindoc/plugin_installation.xml

@@ -1015 +1015 @@
         you to import and export plug-in configurations. This makes
         it easy to copy configurations between servers. The BASE website
-        also has a <ulink url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"
+        also has a <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/admin/plugin_configuration/coreplugins.html"
         >page where you can download additional configurations</ulink>
         not included in the main distribution.

trunk/doc/src/docbook/developerdoc/api_overview.xml

@@ -167 +167 @@
       All information has not yet been transfered from the old documentation.
       The old documentation is available at
-      <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/data/index.html"
-        >http://base.thep.lu.se/chrome/site/doc/development/overview/data/index.html</ulink>
+      <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/data/index.html"
+        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/data/index.html</ulink>
     </note>
     
@@ -2965 +2965 @@
     <para>
       This documentation is only available in the old format.
-      See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/query/index.html"
-        >http://base.thep.lu.se/chrome/site/doc/development/overview/query/index.html</ulink>
+      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html"
+        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html</ulink>
     </para>
     
@@ -2975 +2975 @@
     <para>
       This documentation is only available in the old format.
-      See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/dynamic/index.html"
-        >http://base.thep.lu.se/chrome/site/doc/development/overview/dynamic/index.html</ulink>
+      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html"
+        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html</ulink>
     </para>
   </sect1>

trunk/doc/src/docbook/developerdoc/base_overview.xml

@@ -31 +31 @@
   <para>
     This documentation is only available in the old format.
-    See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/index.html"
-      >http://base.thep.lu.se/chrome/site/doc/development/overview/index.html</ulink>
+    See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/index.html"
+      >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/index.html</ulink>
   </para>
 </chapter>

trunk/doc/src/docbook/developerdoc/core_ref.xml

@@ -40 +40 @@
     <para>
       This documentation is only available in the old format.
-      See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/build.html"
-        >http://base.thep.lu.se/chrome/site/doc/development/build.html</ulink>
+      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/build.html"
+        >http://base.thep.lu.se/chrome/site/doc/historical/development/build.html</ulink>
     </para>
   </sect1>
@@ -227 +227 @@
       <para>
         This documentation is only available in the old format.
-        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/coding/generic.html"
-          >http://base.thep.lu.se/chrome/site/doc/development/coding/generic.html</ulink>
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/coding/generic.html"
+          >http://base.thep.lu.se/chrome/site/doc/historical/development/coding/generic.html</ulink>
       </para>
     </sect2>
@@ -1744 +1744 @@
       <para>
         This documentation is only available in the old format.
-        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/coding/item/index.html"
-          >http://base.thep.lu.se/chrome/site/doc/development/coding/item/index.html</ulink>
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/coding/item/index.html"
+          >http://base.thep.lu.se/chrome/site/doc/historical/development/coding/item/index.html</ulink>
       </para>
     </sect2>    
@@ -1766 +1766 @@
     <para>
       This documentation is only available in the old format.
-      See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/index.html"
-        >http://base.thep.lu.se/chrome/site/doc/development/overview/core/index.html</ulink>
+      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/index.html"
+        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/index.html</ulink>
     </para>
     <sect2 id="core_ref.authentication">
@@ -1773 +1773 @@
       <para>
         This documentation is only available in the old format.
-        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/authentication.html"
-          >http://base.thep.lu.se/chrome/site/doc/development/overview/core/authentication.html</ulink>
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html"
+          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html</ulink>
       </para>
     </sect2>    
@@ -1781 +1781 @@
       <para>
         This documentation is only available in the old format.
-        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/accesspermissions.html"
-          >http://base.thep.lu.se/chrome/site/doc/development/overview/core/accesspermissions.html</ulink>
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html"
+          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html</ulink>
       </para>
     </sect2>    
@@ -1801 +1801 @@
       <para>
         This documentation is only available in the old format.
-        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/itemhandling.html"
-          >http://base.thep.lu.se/chrome/site/doc/development/overview/core/itemhandling.html</ulink>
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html"
+          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html</ulink>
       </para>
     </sect2>    
@@ -1809 +1809 @@
       <para>
         This documentation is only available in the old format.
-        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/batchprocessing.html"
-          >http://base.thep.lu.se/chrome/site/doc/development/overview/core/batchprocessing.html</ulink>
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html"
+          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html</ulink>
       </para>
     </sect2>    
@@ -1823 +1823 @@
       <para>
         This documentation is only available in the old format.
-        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/plugins.html"
-          >http://base.thep.lu.se/chrome/site/doc/development/overview/core/plugins.html</ulink>
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html"
+          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html</ulink>
       </para>
     </sect2>    

trunk/doc/src/docbook/faq/faqs.xml

@@ -450 +450 @@
         <qandaentry>
           <question>
-            <para>
-              I have created a raw bioassay which is not Affymetrix but the system does not
-              allow me to upload a data file whereas it is possible to do so if I
-              declared my rawbioassay of type Affymetrix. Why?
-            </para>
-          </question>
-          <answer>
-            <para>
-              This is normal. BASE deals with Affymetrix data files differently. BASE
-              stores native Affymetrix file and does not load the value in tables as
-              it does for other platforms. See <xref linkend="experiments_analysis.rawbioassay.rawdata" />
-              for more information.
-            </para>
-          </answer>
-        </qandaentry>
-
-        <qandaentry>
-          <question>
-            <para>
-              I have created a raw bioassay using Affymetrix CEL file but the
-              interface says 'no spot'. I have really loaded the file! Why?
-            </para>
-          </question>
-          <answer>
-            <para>
-              Again, this is because of the specific treatment of 
-              Affymetrix files compared to other platforms. Affymetrix data
-              is kept in the files and are not imported into the database.
-              Currently, the number of spots can only be counted when
-              data is located in the database.
-            </para>
-          </answer>
-        </qandaentry>
-
-        <qandaentry>
-          <question>
             <para>Are Affymetrix CDT and CAB files supported by BASE?</para>
           </question>

trunk/doc/src/docbook/overviewdoc/resources.xml

@@ -198 +198 @@
       link to
       <ulink
-        url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html">
+        url="http://base.thep.lu.se/chrome/site/doc/historical/admin/plugin_configuration/coreplugins.html">
         a page that lists the core plug-ins</ulink>.
       All plug-ins that are included in the installation of

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

@@ -1825 +1825 @@
         List<String> setExtraFloats = new ArrayList<String>(); 
         if (ffp.getHeader("setExtraFloats") != null)
+        {
           setExtraFloats = Arrays.asList(ffp.getHeader("setExtraFloats").split("\\t"));
-        
+        }
         ffp.setMinDataColumns(columns.size() - 1 + assays.size() * assayFields.size());
         
@@ -1878 +1879 @@
 
         for (int i = 0; i < intCol.length; ++i)
+        {
           intCol[i] += dataCol;
+        }
         aCol += dataCol;
         mCol += dataCol;
@@ -1904 +1907 @@
         }
         
+        float[] intensities = new float[intCol.length];
         while (ffp.hasMoreData())
         {
@@ -1909 +1913 @@
           FlatFileParser.Data dataline = ffp.nextData();
           int index = 0;
+          Integer position = Values.getInteger(dataline.get(posCol), null);
           for (Integer assayId : assays)
           {
+            // Only insert the spot if all intensity values are correct numbers
+            boolean insertSpot = true;
             short dataCubeColumn = bioAssayColumns.get(assayId);
-            try
+            if (intCols)
             {
-              float[] intensities = new float[intCol.length];
-              Integer position = dataline.get(posCol) == null ? null : new Integer(dataline.get(posCol));
-
-              if (intCols)
+              for (int i = 0; i < intCol.length; ++i)
               {
-                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));
+                float value = Values.getFloat(dataline.get(intCol[i] + index), Float.NaN);
+                insertSpot &= !Float.isNaN(value);
+                intensities[i] = value;
               }
-              else
+            }
+            else
+            {
+              float a = Values.getFloat(dataline.get(aCol + index), Float.NaN);
+              float m = Values.getFloat(dataline.get(mCol + index), Float.NaN);
+              insertSpot = !Float.isNaN(m) && !Float.isNaN(a);
+              if (insertSpot)
               {
-                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));
+                intensities[1] = (float)(Math.pow(10, a) / Math.pow(2, 0.5 * m));
+                intensities[0] = (float)(intensities[1] * Math.pow(2, m));
               }
-
+            }
+            if (insertSpot) 
+            {
               spotBatcher.insert(dataCubeColumn, position, intensities);
-                    
+              // Extra values
               for (int i = 0; i < evBatcher.size(); i++)
               {
-                try
+                float value = Values.getFloat(dataline.get(extraFloatsCol[i] + index), Float.NaN);
+                if (!Float.isNaN(value)) 
                 {
-                  Float ev = new Float(dataline.get(extraFloatsCol[i] + index));
-                  evBatcher.get(i).insert(dataCubeColumn, position, ev);
+                  evBatcher.get(i).insert(dataCubeColumn, position, value);
                 }
-                catch (NumberFormatException e)
-                {}
               }
-              index += assayFields.size();
             }
-            catch (NumberFormatException e)
-            {}
-          }
-        }
-      }
-    }
-
+            index += assayFields.size();
+          }
+        }
+      }
+    }
   }
   

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

@@ -942 +942 @@
       ExtraValueType evt = ev.getExtraValueType();
       items.add(new QueryItem("xtra."+evt.getExternalId(), "[Extra] "+evt.getName(), 
-        "_xc_"+evt.getName(), "xtra('" + evt.getExternalId() + "')", evt.getAverageMethod()));
+        "_xc_"+evt.getExternalId(), "xtra('" + evt.getExternalId() + "')", evt.getAverageMethod()));
     }
     Collections.sort(items, new QueryItemTitleComparator());

trunk/src/test/Base1NullPlugin.java

@@ -69 +69 @@
     while (line != null)
     {
+      if (line.startsWith("assayFields") && line.contains("_xc_"))
+      {
+        /*
+          The file contains extra values. To make the
+          import work we must remove the _xc_ prefix for the
+          extra value columns and add a setExtraFloats header
+        */
+        String[] columns = line.split("\\t");
+        line = "assayFields";
+        String setExtraFloats = "setExtraFloats";
+        for (int i = 1; i < columns.length; ++i)
+        {
+          String column = columns[i];
+          if (column.startsWith("_xc_"))
+          {
+            column = column.substring(4);
+            setExtraFloats += "\t" + column;
+          }
+          line += "\t" + column;
+        }
+        System.out.println(setExtraFloats);
+      }
       System.out.println(line);
       log.println(line);

trunk/src/test/TestAnalyzePluginUtil.java

@@ -25 +25 @@
 import java.util.regex.Pattern;
 
+import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Experiment;
 import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.Platform;
@@ -35 +37 @@
 import net.sf.basedb.core.ReporterBatcher;
 import net.sf.basedb.core.data.RawData;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.Values;
@@ -46 +50 @@
    * @param rawBioAssays number of {@link net.sf.basedb.core.RawBioAssay RawBioAssays} in experiment
    * @param spots number of spots in each RawBioAssay 
+   * @param randomize Randomize imported intensity values by multiplying them with 
+   * a random value between 1+randomize and 1-randomize. Eg. if randomize=0.8, the factory is
+   * a random value between 0.8 and 1.2
   */
-  static int test_createExperiment(String file, int rawBioAssays, int spots)
+  static int test_createExperiment(String file, int rawBioAssays, int spots, float randomize)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.EXPERIMENT)) return 0;
@@ -87 +94 @@
           rawData.setReporter(reporterId == null ? null : reporterBatcher.getByExternalId(reporterId));
           
+          float randomCh1 = (float)((2 * Math.random() - 1) * randomize + 1);
+          float randomCh2 = (float)((2 * Math.random() - 1) * randomize + 1);
+          
           Map<String, Object> extraData = rawData.getAllExtended();
           extraData.put("diameter", Values.getFloat(parsedData.get(7), null));
-          extraData.put("ch1FgMedian", Values.getFloat(parsedData.get(8), null));
-          extraData.put("ch1FgMean", Values.getFloat(parsedData.get(9), null));
-          extraData.put("ch1FgSd", Values.getFloat(parsedData.get(10), null));
-          extraData.put("ch1BgMedian", Values.getFloat(parsedData.get(11), null));
-          extraData.put("ch1BgMean", Values.getFloat(parsedData.get(12), null));
-          extraData.put("ch1BgSd", Values.getFloat(parsedData.get(13), null));
+          extraData.put("ch1FgMedian", randomCh1 * Values.getFloat(parsedData.get(8), null));
+          extraData.put("ch1FgMean", randomCh1 * Values.getFloat(parsedData.get(9), null));
+          extraData.put("ch1FgSd", randomCh1 * Values.getFloat(parsedData.get(10), null));
+          extraData.put("ch1BgMedian", randomCh1 * Values.getFloat(parsedData.get(11), null));
+          extraData.put("ch1BgMean", randomCh1 * Values.getFloat(parsedData.get(12), null));
+          extraData.put("ch1BgSd", randomCh1 * Values.getFloat(parsedData.get(13), null));
           extraData.put("ch1PercSd1", Values.getInteger(parsedData.get(14), null));
           extraData.put("ch1PercSd2", Values.getInteger(parsedData.get(15), null));
           extraData.put("ch1PercSat", Values.getInteger(parsedData.get(16), null));
-          extraData.put("ch2FgMedian", Values.getFloat(parsedData.get(17), null));
-          extraData.put("ch2FgMean", Values.getFloat(parsedData.get(18), null));
-          extraData.put("ch2FgSd", Values.getFloat(parsedData.get(19), null));
-          extraData.put("ch2BgMedian", Values.getFloat(parsedData.get(20), null));
-          extraData.put("ch2BgMean", Values.getFloat(parsedData.get(21), null));
-          extraData.put("ch2BgSd", Values.getFloat(parsedData.get(22), null));
+          extraData.put("ch2FgMedian", randomCh2 * Values.getFloat(parsedData.get(17), null));
+          extraData.put("ch2FgMean", randomCh2 * Values.getFloat(parsedData.get(18), null));
+          extraData.put("ch2FgSd", randomCh2 * Values.getFloat(parsedData.get(19), null));
+          extraData.put("ch2BgMedian", randomCh2 * Values.getFloat(parsedData.get(20), null));
+          extraData.put("ch2BgMean", randomCh2 * Values.getFloat(parsedData.get(21), null));
+          extraData.put("ch2BgSd", randomCh2 * Values.getFloat(parsedData.get(22), null));
           extraData.put("ch2PercSd1", Values.getInteger(parsedData.get(23), null));
           extraData.put("ch2PercSd2", Values.getInteger(parsedData.get(24), null));
@@ -148 +158 @@
         formulaId, rawBioAssayIds);
       TestJob.test_execute(jobId);
-      
+      ItemQuery<BioAssaySet> query = e.getBioAssaySets();
+      query.order(Orders.desc(Hql.property("id")));
+      id = query.iterate(dc).next().getId();
       write("--Create root BioAssaySet in TestAnalyzePluginUtil OK");
     }

trunk/src/test/TestBase1PluginExecuter.java

@@ -16 +16 @@
 import net.sf.basedb.core.PluginResponse;
 import net.sf.basedb.core.RequestInformation;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.core.plugin.Response;
 
@@ -61 +62 @@
     
     // Create experiment
-    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100);
+    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100, 0.8f);
     int[] rawBioAssays = TestExperiment.test_list_rawbioassays(experimentId, -1);
 
@@ -72 +73 @@
     int fileId = TestFile.test_create("data/test.nullplugin.base", false, false);
     int fileId2 = TestFile.test_create("data/test.base1plugin.base", false, false);
+    int fileIdMatrix = TestFile.test_create("data/test.nullplugin.matrix.base", false, false);
     int directoryId = TestDirectory.test_create(true, "Base1PluginExecuter");
     
-    TestAnalyzePluginUtil.test_createRootBioAssaySet(experimentId, formulaId);
+    int rootBioAssaySetId = TestAnalyzePluginUtil.test_createRootBioAssaySet(experimentId, formulaId);
+    int filteredBioAssaySetId = TestExperiment.test_filter_bioassayset(rootBioAssaySetId, 1);
     int pluginDefinitionId = TestPluginDefinition.test_get("net.sf.basedb.plugins.Base1PluginExecuter");
     int pluginConfigurationId = test_create_configuration(pluginDefinitionId, fileId);
     int pluginConfigurationId2 = test_create_configuration(pluginDefinitionId, fileId2);
-    
-    // Copy input to output
-    int jobId = test_create_job(pluginConfigurationId, experimentId, directoryId);
+    int pluginConfigurationIdMatrix = test_create_configuration(pluginDefinitionId, fileIdMatrix);
+    
+    // Calculate extra value
+    int aExtraValueId = TestExtraValueType.test_create("a", Type.FLOAT, false);
+    TestExperiment.test_calculate_spotextravalues(rootBioAssaySetId, false, 0, aExtraValueId, 0);
+    TestExperiment.test_calculate_spotextravalues(filteredBioAssaySetId, false, 0, aExtraValueId, 0);
+    
+    // Copy input to output - serial format
+    int jobId = test_create_job(pluginConfigurationId, experimentId, rootBioAssaySetId, directoryId);
     TestJob.test_execute(jobId);
     
+    // Copy input to output - matrix format
+    int jobIdMatrix = test_create_job(pluginConfigurationIdMatrix, experimentId, rootBioAssaySetId, directoryId);
+    TestJob.test_execute(jobIdMatrix);
+    
+    // Copy input to output - matrix format - filtered bioassayset
+    int jobIdMatrix2 = test_create_job(pluginConfigurationIdMatrix, experimentId, filteredBioAssaySetId, directoryId);
+    TestJob.test_execute(jobIdMatrix2);
+    
     // One-to-one mapping on assays and reporters
-    int jobId2 = test_create_job(pluginConfigurationId2, experimentId, directoryId);
+    int jobId2 = test_create_job(pluginConfigurationIdMatrix, experimentId, rootBioAssaySetId, directoryId);
     TestJob.test_execute(jobId2);
 
     // Merge assays
-    int jobId3 = test_create_job(pluginConfigurationId2, experimentId, directoryId, 
+    int jobId3 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId, 
         new Parameter("mergeAssays", "1"));
     TestJob.test_execute(jobId3);
 
     // Offset positions
-    int jobId4 = test_create_job(pluginConfigurationId2, experimentId, directoryId, 
+    int jobId4 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId, 
         new Parameter("offsetPositions", "1"));
     TestJob.test_execute(jobId4);
 
     // Offset positions and merge assays
-    int jobId5 = test_create_job(pluginConfigurationId2, experimentId, directoryId, 
+    int jobId5 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId, 
         new Parameter("mergeAssays", "1"), new Parameter("offsetPositions", "1"));
     TestJob.test_execute(jobId5);
 
     // Create reporter list
-    int jobId6 = test_create_job(pluginConfigurationId2, experimentId, directoryId,
+    int jobId6 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId,
         new Parameter("reporterList", "1"));
     TestJob.test_execute(jobId6);
@@ -118 +135 @@
       }
     }
+    TestExtraValueType.test_delete(aExtraValueId);
     TestPluginConfiguration.test_delete(pluginConfigurationId);
     TestPluginConfiguration.test_delete(pluginConfigurationId2);
+    TestPluginConfiguration.test_delete(pluginConfigurationIdMatrix);
     TestFormula.test_delete(formulaId);
     TestFormula.test_delete(formulaChromosomeId);
     TestFile.test_delete(fileId);
     TestFile.test_delete(fileId2);
+    TestFile.test_delete(fileIdMatrix);
     TestDirectory.test_delete(directoryId, true);
     TestReporter.test_delete();
@@ -175 +195 @@
   }
   
-  static int test_create_job(int pluginConfigurationId, int experimentId, int directoryId, Parameter... parameters)
+  static int test_create_job(int pluginConfigurationId, int experimentId, int bioAssaySetId, int directoryId, Parameter... parameters)
   {
     if (pluginConfigurationId == 0 || !TestUtil.hasPermission(Permission.CREATE, Item.JOB)) return 0;
@@ -185 +205 @@
 
       Experiment e = Experiment.getById(dc, experimentId);
-      BioAssaySet bioAssaySet = e.getBioAssaySets().iterate(dc).next();
+      BioAssaySet bioAssaySet = BioAssaySet.getById(dc, bioAssaySetId);
       
       PluginConfiguration pc = PluginConfiguration.getById(dc, pluginConfigurationId);

trunk/src/test/TestBioAsssaySetExporter.java

@@ -109 +109 @@
       TestExperiment.test_add_rawbioassay(experiment, rba2);
       bas = TestExperiment.test_create_root_bioassayset_using_calculator(experiment, "medianfg", new int[] {rba1, rba2});
-      TestExperiment.test_calculate_spotextravalues(bas, 0, 0, 0);
       
       test_exportBaseFile(bas, file, false, false);

trunk/src/test/TestExperiment.java

@@ -108 +108 @@
     
     
-    int filterBasId = test_filter_bioassayset(rootBasId);
+    int filterBasId = test_filter_bioassayset(rootBasId, 2.0f);
     int basId = test_create_bioassayset(filterBasId);
     
@@ -115 +115 @@
     int stringExtraId = TestExtraValueType.test_create("test.string", Type.STRING, false);
     
-    int extraSpotId = test_calculate_spotextravalues(filterBasId, intExtraId, floatExtraId, stringExtraId);
+    int extraSpotId = test_calculate_spotextravalues(filterBasId, true,
+        intExtraId, floatExtraId, stringExtraId);
     int extraPosId = test_calculate_positionextravalues(filterBasId, intExtraId, floatExtraId, stringExtraId);
     // TODO 
@@ -932 +933 @@
   }
 
-  static int test_filter_bioassayset(int bioAssaySetId)
+  static int test_filter_bioassayset(int bioAssaySetId, float factor)
   {
     if (bioAssaySetId == 0) return 0;
@@ -961 +962 @@
         )
       );
-      query.setParameter("factor", 2, Type.INT);
+      query.setParameter("factor", factor, Type.FLOAT);
       
       FilterBatcher filterBatcher = bas.getFilterBatcher();
@@ -996 +997 @@
   }
 
-  static int test_calculate_spotextravalues(int bioAssaySetId, int intExtraId, int floatExtraId, int stringExtraId)
+  static int test_calculate_spotextravalues(int bioAssaySetId, boolean createChild, 
+      int intExtraId, int floatExtraId, int stringExtraId)
   {
     if (bioAssaySetId == 0) return 0;
@@ -1006 +1008 @@
       BioAssaySet source = BioAssaySet.getById(dc, bioAssaySetId);
       
-      Transformation t = source.newTransformation(null);
-      dc.saveItem(t);
-
-      BioAssaySet bas = t.newProduct(null, null, true);
-      bas.setName("Extra spot values bioassayset");
-      dc.saveItem(bas);
+      BioAssaySet insertTo = source;
+      if (createChild)
+      {
+        Transformation t = source.newTransformation(null);
+        dc.saveItem(t);
+  
+        insertTo = t.newProduct(null, null, true);
+        insertTo.setName("Extra spot values bioassayset");
+        dc.saveItem(insertTo);
+      }
 
       SpotExtraValueBatcher<Integer> intBatcher = null;
@@ -1017 +1023 @@
       {
         ExtraValueType intExtraValue = ExtraValueType.getById(dc, intExtraId);
-        intBatcher = bas.getSpotExtraValueBatcher(Integer.class, intExtraValue, null);
+        intBatcher = insertTo.getSpotExtraValueBatcher(Integer.class, intExtraValue, null);
       }
       SpotExtraValueBatcher<Float> floatBatcher = null;
@@ -1023 +1029 @@
       {
         ExtraValueType floatExtraValue = ExtraValueType.getById(dc, floatExtraId);
-        floatBatcher = bas.getSpotExtraValueBatcher(Float.class, floatExtraValue, null);
+        floatBatcher = insertTo.getSpotExtraValueBatcher(Float.class, floatExtraValue, null);
       }
       SpotExtraValueBatcher<String> stringBatcher = null;
@@ -1029 +1035 @@
       {
         ExtraValueType stringExtraValue = ExtraValueType.getById(dc, stringExtraId);
-        stringBatcher = bas.getSpotExtraValueBatcher(String.class, stringExtraValue, null);
+        stringBatcher = insertTo.getSpotExtraValueBatcher(String.class, stringExtraValue, null);
       }
       
@@ -1064 +1070 @@
 
       dc.commit();
-      id = bas.getId();
-      dc = TestUtil.getDbControl();
-      dc.reattachItem(bas);
-      write_item(0, bas);
+      id = insertTo.getId();
+      dc = TestUtil.getDbControl();
+      dc.reattachItem(insertTo);
+      write_item(0, insertTo);
       write("--Calculate spot extra values OK ("+numSpots+" values inserted)");
 

trunk/src/test/TestLowessNormalization.java

@@ -52 +52 @@
   {
     write("++Testing TestLowessNormalization");
-    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100);
+    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100, 1.0f);
 
     int formulaId = TestFormula.test_create(null, Formula.Type.INTENSITY_EXPRESSION,

trunk/src/test/TestMedianRatioNormalization.java

@@ -51 +51 @@
   {
     write("++Testing MedianRatioNormalization");
-    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100);
+    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100, 1.0f);
     int formulaId = TestFormula.test_create(null, Formula.Type.INTENSITY_EXPRESSION,
         "genepix", new String[] { "raw('ch1FgMedian')", "raw('ch2FgMedian')" }, false);

trunk/src/test/data/test.nullplugin.base

@@ -1 +1 @@
 BASEfile
 section plugin
-uniqueName  onk.lu.se/enell/wget
+uniqueName  nullplugin-serial
 versionNumber 1.0
 name  Base1NullPlugin

trunk/www/admin/plugindefinitions/select_installation_type.jsp

@@ -87 +87 @@
   </base:head>
   <base:body onload="init()">
-    <form name="installations" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="installations" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="cmd" value="InstallationType">

trunk/www/admin/softwaretypes/view_softwaretype.jsp

@@ -113 +113 @@
         onclick="newSoftware()"
         title="New software…"
-        tooltip="Create a new hardware of this type"
+        tooltip="Create a new software of this type"
         visible="<%=sc.hasPermission(Permission.CREATE, Item.SOFTWARE) && usePermission%>"
       />

trunk/www/biomaterials/samples/list_samples.jsp

@@ -634 +634 @@
                     image="add.png" 
                     onclick="<%="newExtract("+itemId+")"%>" 
-                    tooltip="Create new sample" 
+                    tooltip="Create new extract" 
                     visible="<%=mode.hasEditLink() && createExtractPermission && usePermission %>"
                   />

trunk/www/common/columns/confirm_delete.jsp

@@ -48 +48 @@
   </base:note>
   <p>
-  <form action="submit_preset.jsp" method="get" name="confirm">
+  <form action="submit_preset.jsp" method="post" name="confirm">
     <input type=hidden name="ID" value="<%=ID%>">
     <input type=hidden name="cmd" value="Delete">

trunk/www/common/columns/save_preset.jsp

@@ -86 +86 @@
 <base:body onload="init()">
   <p>
-  <form name="preset" action="submit_preset.jsp" method="get" onsubmit="return validateForm();">
+  <form name="preset" action="submit_preset.jsp" method="post" onsubmit="return validateForm();">
   <input type="hidden" name="ID" value="<%=ID%>">
   <input type="hidden" name="cmd" value="Save">

trunk/www/common/context/saveas.jsp

@@ -77 +77 @@
 <base:body onload="init()">
   <p>
-  <form name="preset" action="index.jsp" method="get" onsubmit="return validateForm();">
+  <form name="preset" action="index.jsp" method="post" onsubmit="return validateForm();">
   <input type=hidden name="ID" value="<%=ID%>">
   <input type=hidden name="cmd" value="SaveCurrentContext">

trunk/www/common/import/no_fileformat.jsp

@@ -104 +104 @@
   </base:head>
   <base:body>
-    <form name="import" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="import" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="cmd" value="AutoDetect">

trunk/www/common/import/select_plugin.jsp

@@ -212 +212 @@
   </base:head>
   <base:body onload="init()">
-    <form name="import" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="import" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="cmd" value="RunPlugin">

trunk/www/common/plugin/finish_job.jsp

@@ -106 +106 @@
   </base:head>
   <base:body>
-    <form name="plugin" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="plugin" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="cmd" value="FinishNewJob">

trunk/www/common/plugin/select_plugin.jsp

@@ -194 +194 @@
   </base:head>
   <base:body onload="init()">
-    <form name="plugin" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="plugin" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="cmd" value="NewJob">

trunk/www/logout.jsp

@@ -79 +79 @@
 <base:body>
   <br>
-  <form action="logout.jsp" method="get" name="logout" onsubmit="return false;">
+  <form action="logout.jsp" method="post" name="logout" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="noconfirm" value="1">

trunk/www/plugins/net/sf/basedb/clients/web/plugins/simple_export.jsp

@@ -251 +251 @@
   </base:head>
   <base:body onload="init()">
-    <form name="export" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="export" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">

trunk/www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp

@@ -284 +284 @@
   </base:head>
   <base:body onload="init()">
-    <form name="extraValue" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="extraValue" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">

trunk/www/plugins/net/sf/basedb/plugins/jep_filter.jsp

@@ -291 +291 @@
   </base:head>
   <base:body onload="init()">
-    <form name="filter" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="filter" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">

trunk/www/plugins/net/sf/basedb/plugins/jep_intensity_transformer.jsp

@@ -165 +165 @@
   </base:head>
   <base:body onload="init()">
-    <form name="transformation" action="index.jsp" method="get" onsubmit="return false;">
+    <form name="transformation" action="index.jsp" method="post" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
     <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">

trunk/www/views/experiments/overview/save_preset.jsp

@@ -85 +85 @@
 <base:body onload="init()">
   <p>
-  <form name="preset" action="index.jsp" method="get" onsubmit="return validateForm();">
+  <form name="preset" action="index.jsp" method="post" onsubmit="return validateForm();">
   <input type="hidden" name="ID" value="<%=ID%>">
   <input type="hidden" name="cmd" value="Save">