Changeset 4537


Ignore:
Timestamp:
Sep 18, 2008, 11:23:28 AM (14 years ago)
Author:
Nicklas Nordborg
Message:

Merged patch release 2.8.2 to the trunk

Location:
trunk
Files:
37 edited
3 copied

Legend:

Unmodified
Added
Removed
  • trunk/build.xml

    r4508 r4537  
    14051405      <!--fileset dir="doc" includes="development/**/*" /-->
    14061406      <fileset dir="doc" includes="licenses/**/*" />
    1407       <fileset dir="doc" includes="specifications/**/*" />
     1407      <fileset dir="doc" includes="historical/admin/**/*" />
     1408      <fileset dir="doc" includes="historical/development/**/*" />
     1409      <fileset dir="doc" includes="historical/specifications/**/*" />
    14081410      <!--fileset dir="doc" includes="user/**/*" /-->
    14091411      <fileset dir="doc" includes="*.*" />
  • trunk/credits.txt

    r4508 r4537  
    2626USA.
    2727
    28 The current BASE team is (at BASE 2.8.1 release)
     28The current BASE team is (at BASE 2.8.2 release)
    2929
    3030Jari Häkkinen
  • trunk/doc/src/docbook/admindoc/extensions.xml

    r4509 r4537  
    6565      folder. This is the only place were extensions can be installed.
    6666    </para>
     67   
     68    <note>
     69      <title>Make sure the extensions folder is writable by Tomcat</title>
     70      <para>
     71        The extension you are installing may include resources such as HTML
     72        files, JSP scripts, images, etc. that needs to be extracted to the
     73        web application path before they can be used. This extraction is
     74        automatically done by the extensions system, but you have to make
     75        sure that the user account Tomcat is running as has permission
     76        to create (and delete) new files in the
     77        <filename class="directory">&lt;base-dir&gt;/www/extensions</filename>
     78        directory.
     79      </para>
     80    </note>
    6781   
    6882    <para>
  • trunk/doc/src/docbook/admindoc/installation_upgrade.xml

    r4509 r4537  
    833833              is available in the
    834834              <ulink
    835               url="http://base.thep.lu.se/chrome/site/doc/development/build.html">building
     835              url="http://base.thep.lu.se/chrome/site/doc/historical/development/build.html">building
    836836              BASE document</ulink>. When you return back after
    837837              compiling in the subversion tree you can follow the
     
    976976            There is an
    977977            administrator <ulink
    978             url="http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html">document
     978            url="http://base.thep.lu.se/chrome/site/doc/historical/admin/extended-properties.html">document
    979979            discussing extended properties</ulink> available. If you
    980980            plan to perform a migration of a BASE version 1.2 database you
     
    10271027<programlisting>cd /path/to/tomcat/webapps
    10281028ln -s /path_to_base/www base2</programlisting>
     1029          </para>
     1030          <para>
     1031            If you plan to install extensions you should make sure that
     1032            the <filename class="directory">&lt;base-dir&gt;/www/extensions</filename>
     1033            directory is writable by the user account Tomcat is running as.
     1034          </para>
     1035          <para>
    10291036            Start/restart Tomcat, and try http://hostname:8080/base2
    10301037            (change <emphasis>hostname</emphasis> to your hostname) in
  • trunk/doc/src/docbook/admindoc/plugin_installation.xml

    r4509 r4537  
    10151015        you to import and export plug-in configurations. This makes
    10161016        it easy to copy configurations between servers. The BASE website
    1017         also has a <ulink url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"
     1017        also has a <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/admin/plugin_configuration/coreplugins.html"
    10181018        >page where you can download additional configurations</ulink>
    10191019        not included in the main distribution.
  • trunk/doc/src/docbook/developerdoc/api_overview.xml

    r4509 r4537  
    167167      All information has not yet been transfered from the old documentation.
    168168      The old documentation is available at
    169       <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/data/index.html"
    170         >http://base.thep.lu.se/chrome/site/doc/development/overview/data/index.html</ulink>
     169      <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/data/index.html"
     170        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/data/index.html</ulink>
    171171    </note>
    172172   
     
    29652965    <para>
    29662966      This documentation is only available in the old format.
    2967       See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/query/index.html"
    2968         >http://base.thep.lu.se/chrome/site/doc/development/overview/query/index.html</ulink>
     2967      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html"
     2968        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html</ulink>
    29692969    </para>
    29702970   
     
    29752975    <para>
    29762976      This documentation is only available in the old format.
    2977       See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/dynamic/index.html"
    2978         >http://base.thep.lu.se/chrome/site/doc/development/overview/dynamic/index.html</ulink>
     2977      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html"
     2978        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html</ulink>
    29792979    </para>
    29802980  </sect1>
  • trunk/doc/src/docbook/developerdoc/base_overview.xml

    r4509 r4537  
    3131  <para>
    3232    This documentation is only available in the old format.
    33     See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/index.html"
    34       >http://base.thep.lu.se/chrome/site/doc/development/overview/index.html</ulink>
     33    See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/index.html"
     34      >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/index.html</ulink>
    3535  </para>
    3636</chapter>
  • trunk/doc/src/docbook/developerdoc/core_ref.xml

    r4509 r4537  
    4040    <para>
    4141      This documentation is only available in the old format.
    42       See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/build.html"
    43         >http://base.thep.lu.se/chrome/site/doc/development/build.html</ulink>
     42      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/build.html"
     43        >http://base.thep.lu.se/chrome/site/doc/historical/development/build.html</ulink>
    4444    </para>
    4545  </sect1>
     
    227227      <para>
    228228        This documentation is only available in the old format.
    229         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/coding/generic.html"
    230           >http://base.thep.lu.se/chrome/site/doc/development/coding/generic.html</ulink>
     229        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/coding/generic.html"
     230          >http://base.thep.lu.se/chrome/site/doc/historical/development/coding/generic.html</ulink>
    231231      </para>
    232232    </sect2>
     
    17441744      <para>
    17451745        This documentation is only available in the old format.
    1746         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/coding/item/index.html"
    1747           >http://base.thep.lu.se/chrome/site/doc/development/coding/item/index.html</ulink>
     1746        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/coding/item/index.html"
     1747          >http://base.thep.lu.se/chrome/site/doc/historical/development/coding/item/index.html</ulink>
    17481748      </para>
    17491749    </sect2>   
     
    17661766    <para>
    17671767      This documentation is only available in the old format.
    1768       See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/index.html"
    1769         >http://base.thep.lu.se/chrome/site/doc/development/overview/core/index.html</ulink>
     1768      See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/index.html"
     1769        >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/index.html</ulink>
    17701770    </para>
    17711771    <sect2 id="core_ref.authentication">
     
    17731773      <para>
    17741774        This documentation is only available in the old format.
    1775         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/authentication.html"
    1776           >http://base.thep.lu.se/chrome/site/doc/development/overview/core/authentication.html</ulink>
     1775        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html"
     1776          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html</ulink>
    17771777      </para>
    17781778    </sect2>   
     
    17811781      <para>
    17821782        This documentation is only available in the old format.
    1783         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/accesspermissions.html"
    1784           >http://base.thep.lu.se/chrome/site/doc/development/overview/core/accesspermissions.html</ulink>
     1783        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html"
     1784          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html</ulink>
    17851785      </para>
    17861786    </sect2>   
     
    18011801      <para>
    18021802        This documentation is only available in the old format.
    1803         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/itemhandling.html"
    1804           >http://base.thep.lu.se/chrome/site/doc/development/overview/core/itemhandling.html</ulink>
     1803        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html"
     1804          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html</ulink>
    18051805      </para>
    18061806    </sect2>   
     
    18091809      <para>
    18101810        This documentation is only available in the old format.
    1811         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/batchprocessing.html"
    1812           >http://base.thep.lu.se/chrome/site/doc/development/overview/core/batchprocessing.html</ulink>
     1811        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html"
     1812          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html</ulink>
    18131813      </para>
    18141814    </sect2>   
     
    18231823      <para>
    18241824        This documentation is only available in the old format.
    1825         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/overview/core/plugins.html"
    1826           >http://base.thep.lu.se/chrome/site/doc/development/overview/core/plugins.html</ulink>
     1825        See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html"
     1826          >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html</ulink>
    18271827      </para>
    18281828    </sect2>   
  • trunk/doc/src/docbook/faq/faqs.xml

    r4509 r4537  
    450450        <qandaentry>
    451451          <question>
    452             <para>
    453               I have created a raw bioassay which is not Affymetrix but the system does not
    454               allow me to upload a data file whereas it is possible to do so if I
    455               declared my rawbioassay of type Affymetrix. Why?
    456             </para>
    457           </question>
    458           <answer>
    459             <para>
    460               This is normal. BASE deals with Affymetrix data files differently. BASE
    461               stores native Affymetrix file and does not load the value in tables as
    462               it does for other platforms. See <xref linkend="experiments_analysis.rawbioassay.rawdata" />
    463               for more information.
    464             </para>
    465           </answer>
    466         </qandaentry>
    467 
    468         <qandaentry>
    469           <question>
    470             <para>
    471               I have created a raw bioassay using Affymetrix CEL file but the
    472               interface says 'no spot'. I have really loaded the file! Why?
    473             </para>
    474           </question>
    475           <answer>
    476             <para>
    477               Again, this is because of the specific treatment of
    478               Affymetrix files compared to other platforms. Affymetrix data
    479               is kept in the files and are not imported into the database.
    480               Currently, the number of spots can only be counted when
    481               data is located in the database.
    482             </para>
    483           </answer>
    484         </qandaentry>
    485 
    486         <qandaentry>
    487           <question>
    488452            <para>Are Affymetrix CDT and CAB files supported by BASE?</para>
    489453          </question>
  • trunk/doc/src/docbook/overviewdoc/resources.xml

    r4509 r4537  
    198198      link to
    199199      <ulink
    200         url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html">
     200        url="http://base.thep.lu.se/chrome/site/doc/historical/admin/plugin_configuration/coreplugins.html">
    201201        a page that lists the core plug-ins</ulink>.
    202202      All plug-ins that are included in the installation of
  • trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

    r4532 r4537  
    18251825        List<String> setExtraFloats = new ArrayList<String>();
    18261826        if (ffp.getHeader("setExtraFloats") != null)
     1827        {
    18271828          setExtraFloats = Arrays.asList(ffp.getHeader("setExtraFloats").split("\\t"));
    1828        
     1829        }
    18291830        ffp.setMinDataColumns(columns.size() - 1 + assays.size() * assayFields.size());
    18301831       
     
    18781879
    18791880        for (int i = 0; i < intCol.length; ++i)
     1881        {
    18801882          intCol[i] += dataCol;
     1883        }
    18811884        aCol += dataCol;
    18821885        mCol += dataCol;
     
    19041907        }
    19051908       
     1909        float[] intensities = new float[intCol.length];
    19061910        while (ffp.hasMoreData())
    19071911        {
     
    19091913          FlatFileParser.Data dataline = ffp.nextData();
    19101914          int index = 0;
     1915          Integer position = Values.getInteger(dataline.get(posCol), null);
    19111916          for (Integer assayId : assays)
    19121917          {
     1918            // Only insert the spot if all intensity values are correct numbers
     1919            boolean insertSpot = true;
    19131920            short dataCubeColumn = bioAssayColumns.get(assayId);
    1914             try
     1921            if (intCols)
    19151922            {
    1916               float[] intensities = new float[intCol.length];
    1917               Integer position = dataline.get(posCol) == null ? null : new Integer(dataline.get(posCol));
    1918 
    1919               if (intCols)
     1923              for (int i = 0; i < intCol.length; ++i)
    19201924              {
    1921                 for (int i = 0; i < intCol.length; ++i)
    1922                   intensities[i] = dataline.get(intCol[i] + index) == null ? Float.NaN : new Float(dataline.get(intCol[i] + index));
     1925                float value = Values.getFloat(dataline.get(intCol[i] + index), Float.NaN);
     1926                insertSpot &= !Float.isNaN(value);
     1927                intensities[i] = value;
    19231928              }
    1924               else
     1929            }
     1930            else
     1931            {
     1932              float a = Values.getFloat(dataline.get(aCol + index), Float.NaN);
     1933              float m = Values.getFloat(dataline.get(mCol + index), Float.NaN);
     1934              insertSpot = !Float.isNaN(m) && !Float.isNaN(a);
     1935              if (insertSpot)
    19251936              {
    1926                 float a = dataline.get(aCol + index) == null ? Float.NaN : new Float(dataline.get(aCol + index));
    1927                 float m = dataline.get(mCol + index) == null ? Float.NaN : new Float(dataline.get(mCol + index));
    1928 
    19291937                // int2 = 10^a / 2^(0.5*m)
    19301938                // int1 = int2 * 2^m
    1931                 intensities[1] = new Float(Math.pow(10, a) / Math.pow(2, 0.5 * m));
    1932                 intensities[0] = new Float(intensities[1] * Math.pow(2, m));
     1939                intensities[1] = (float)(Math.pow(10, a) / Math.pow(2, 0.5 * m));
     1940                intensities[0] = (float)(intensities[1] * Math.pow(2, m));
    19331941              }
    1934 
     1942            }
     1943            if (insertSpot)
     1944            {
    19351945              spotBatcher.insert(dataCubeColumn, position, intensities);
    1936                    
     1946              // Extra values
    19371947              for (int i = 0; i < evBatcher.size(); i++)
    19381948              {
    1939                 try
     1949                float value = Values.getFloat(dataline.get(extraFloatsCol[i] + index), Float.NaN);
     1950                if (!Float.isNaN(value))
    19401951                {
    1941                   Float ev = new Float(dataline.get(extraFloatsCol[i] + index));
    1942                   evBatcher.get(i).insert(dataCubeColumn, position, ev);
     1952                  evBatcher.get(i).insert(dataCubeColumn, position, value);
    19431953                }
    1944                 catch (NumberFormatException e)
    1945                 {}
    19461954              }
    1947               index += assayFields.size();
    19481955            }
    1949             catch (NumberFormatException e)
    1950             {}
    1951           }
    1952         }
    1953       }
    1954     }
    1955 
     1956            index += assayFields.size();
     1957          }
     1958        }
     1959      }
     1960    }
    19561961  }
    19571962 
  • trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

    r4523 r4537  
    942942      ExtraValueType evt = ev.getExtraValueType();
    943943      items.add(new QueryItem("xtra."+evt.getExternalId(), "[Extra] "+evt.getName(),
    944         "_xc_"+evt.getName(), "xtra('" + evt.getExternalId() + "')", evt.getAverageMethod()));
     944        "_xc_"+evt.getExternalId(), "xtra('" + evt.getExternalId() + "')", evt.getAverageMethod()));
    945945    }
    946946    Collections.sort(items, new QueryItemTitleComparator());
  • trunk/src/test/Base1NullPlugin.java

    r4514 r4537  
    6969    while (line != null)
    7070    {
     71      if (line.startsWith("assayFields") && line.contains("_xc_"))
     72      {
     73        /*
     74          The file contains extra values. To make the
     75          import work we must remove the _xc_ prefix for the
     76          extra value columns and add a setExtraFloats header
     77        */
     78        String[] columns = line.split("\\t");
     79        line = "assayFields";
     80        String setExtraFloats = "setExtraFloats";
     81        for (int i = 1; i < columns.length; ++i)
     82        {
     83          String column = columns[i];
     84          if (column.startsWith("_xc_"))
     85          {
     86            column = column.substring(4);
     87            setExtraFloats += "\t" + column;
     88          }
     89          line += "\t" + column;
     90        }
     91        System.out.println(setExtraFloats);
     92      }
    7193      System.out.println(line);
    7294      log.println(line);
  • trunk/src/test/TestAnalyzePluginUtil.java

    r4514 r4537  
    2525import java.util.regex.Pattern;
    2626
     27import net.sf.basedb.core.BioAssaySet;
    2728import net.sf.basedb.core.DbControl;
    2829import net.sf.basedb.core.Experiment;
    2930import net.sf.basedb.core.Item;
     31import net.sf.basedb.core.ItemQuery;
    3032import net.sf.basedb.core.Permission;
    3133import net.sf.basedb.core.Platform;
     
    3537import net.sf.basedb.core.ReporterBatcher;
    3638import net.sf.basedb.core.data.RawData;
     39import net.sf.basedb.core.query.Hql;
     40import net.sf.basedb.core.query.Orders;
    3741import net.sf.basedb.util.FileUtil;
    3842import net.sf.basedb.util.Values;
     
    4650   * @param rawBioAssays number of {@link net.sf.basedb.core.RawBioAssay RawBioAssays} in experiment
    4751   * @param spots number of spots in each RawBioAssay
     52   * @param randomize Randomize imported intensity values by multiplying them with
     53   * a random value between 1+randomize and 1-randomize. Eg. if randomize=0.8, the factory is
     54   * a random value between 0.8 and 1.2
    4855  */
    49   static int test_createExperiment(String file, int rawBioAssays, int spots)
     56  static int test_createExperiment(String file, int rawBioAssays, int spots, float randomize)
    5057  {
    5158    if (!TestUtil.hasPermission(Permission.CREATE, Item.EXPERIMENT)) return 0;
     
    8794          rawData.setReporter(reporterId == null ? null : reporterBatcher.getByExternalId(reporterId));
    8895         
     96          float randomCh1 = (float)((2 * Math.random() - 1) * randomize + 1);
     97          float randomCh2 = (float)((2 * Math.random() - 1) * randomize + 1);
     98         
    8999          Map<String, Object> extraData = rawData.getAllExtended();
    90100          extraData.put("diameter", Values.getFloat(parsedData.get(7), null));
    91           extraData.put("ch1FgMedian", Values.getFloat(parsedData.get(8), null));
    92           extraData.put("ch1FgMean", Values.getFloat(parsedData.get(9), null));
    93           extraData.put("ch1FgSd", Values.getFloat(parsedData.get(10), null));
    94           extraData.put("ch1BgMedian", Values.getFloat(parsedData.get(11), null));
    95           extraData.put("ch1BgMean", Values.getFloat(parsedData.get(12), null));
    96           extraData.put("ch1BgSd", Values.getFloat(parsedData.get(13), null));
     101          extraData.put("ch1FgMedian", randomCh1 * Values.getFloat(parsedData.get(8), null));
     102          extraData.put("ch1FgMean", randomCh1 * Values.getFloat(parsedData.get(9), null));
     103          extraData.put("ch1FgSd", randomCh1 * Values.getFloat(parsedData.get(10), null));
     104          extraData.put("ch1BgMedian", randomCh1 * Values.getFloat(parsedData.get(11), null));
     105          extraData.put("ch1BgMean", randomCh1 * Values.getFloat(parsedData.get(12), null));
     106          extraData.put("ch1BgSd", randomCh1 * Values.getFloat(parsedData.get(13), null));
    97107          extraData.put("ch1PercSd1", Values.getInteger(parsedData.get(14), null));
    98108          extraData.put("ch1PercSd2", Values.getInteger(parsedData.get(15), null));
    99109          extraData.put("ch1PercSat", Values.getInteger(parsedData.get(16), null));
    100           extraData.put("ch2FgMedian", Values.getFloat(parsedData.get(17), null));
    101           extraData.put("ch2FgMean", Values.getFloat(parsedData.get(18), null));
    102           extraData.put("ch2FgSd", Values.getFloat(parsedData.get(19), null));
    103           extraData.put("ch2BgMedian", Values.getFloat(parsedData.get(20), null));
    104           extraData.put("ch2BgMean", Values.getFloat(parsedData.get(21), null));
    105           extraData.put("ch2BgSd", Values.getFloat(parsedData.get(22), null));
     110          extraData.put("ch2FgMedian", randomCh2 * Values.getFloat(parsedData.get(17), null));
     111          extraData.put("ch2FgMean", randomCh2 * Values.getFloat(parsedData.get(18), null));
     112          extraData.put("ch2FgSd", randomCh2 * Values.getFloat(parsedData.get(19), null));
     113          extraData.put("ch2BgMedian", randomCh2 * Values.getFloat(parsedData.get(20), null));
     114          extraData.put("ch2BgMean", randomCh2 * Values.getFloat(parsedData.get(21), null));
     115          extraData.put("ch2BgSd", randomCh2 * Values.getFloat(parsedData.get(22), null));
    106116          extraData.put("ch2PercSd1", Values.getInteger(parsedData.get(23), null));
    107117          extraData.put("ch2PercSd2", Values.getInteger(parsedData.get(24), null));
     
    148158        formulaId, rawBioAssayIds);
    149159      TestJob.test_execute(jobId);
    150      
     160      ItemQuery<BioAssaySet> query = e.getBioAssaySets();
     161      query.order(Orders.desc(Hql.property("id")));
     162      id = query.iterate(dc).next().getId();
    151163      write("--Create root BioAssaySet in TestAnalyzePluginUtil OK");
    152164    }
  • trunk/src/test/TestBase1PluginExecuter.java

    r4514 r4537  
    1616import net.sf.basedb.core.PluginResponse;
    1717import net.sf.basedb.core.RequestInformation;
     18import net.sf.basedb.core.Type;
    1819import net.sf.basedb.core.plugin.Response;
    1920
     
    6162   
    6263    // Create experiment
    63     int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100);
     64    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100, 0.8f);
    6465    int[] rawBioAssays = TestExperiment.test_list_rawbioassays(experimentId, -1);
    6566
     
    7273    int fileId = TestFile.test_create("data/test.nullplugin.base", false, false);
    7374    int fileId2 = TestFile.test_create("data/test.base1plugin.base", false, false);
     75    int fileIdMatrix = TestFile.test_create("data/test.nullplugin.matrix.base", false, false);
    7476    int directoryId = TestDirectory.test_create(true, "Base1PluginExecuter");
    7577   
    76     TestAnalyzePluginUtil.test_createRootBioAssaySet(experimentId, formulaId);
     78    int rootBioAssaySetId = TestAnalyzePluginUtil.test_createRootBioAssaySet(experimentId, formulaId);
     79    int filteredBioAssaySetId = TestExperiment.test_filter_bioassayset(rootBioAssaySetId, 1);
    7780    int pluginDefinitionId = TestPluginDefinition.test_get("net.sf.basedb.plugins.Base1PluginExecuter");
    7881    int pluginConfigurationId = test_create_configuration(pluginDefinitionId, fileId);
    7982    int pluginConfigurationId2 = test_create_configuration(pluginDefinitionId, fileId2);
    80    
    81     // Copy input to output
    82     int jobId = test_create_job(pluginConfigurationId, experimentId, directoryId);
     83    int pluginConfigurationIdMatrix = test_create_configuration(pluginDefinitionId, fileIdMatrix);
     84   
     85    // Calculate extra value
     86    int aExtraValueId = TestExtraValueType.test_create("a", Type.FLOAT, false);
     87    TestExperiment.test_calculate_spotextravalues(rootBioAssaySetId, false, 0, aExtraValueId, 0);
     88    TestExperiment.test_calculate_spotextravalues(filteredBioAssaySetId, false, 0, aExtraValueId, 0);
     89   
     90    // Copy input to output - serial format
     91    int jobId = test_create_job(pluginConfigurationId, experimentId, rootBioAssaySetId, directoryId);
    8392    TestJob.test_execute(jobId);
    8493   
     94    // Copy input to output - matrix format
     95    int jobIdMatrix = test_create_job(pluginConfigurationIdMatrix, experimentId, rootBioAssaySetId, directoryId);
     96    TestJob.test_execute(jobIdMatrix);
     97   
     98    // Copy input to output - matrix format - filtered bioassayset
     99    int jobIdMatrix2 = test_create_job(pluginConfigurationIdMatrix, experimentId, filteredBioAssaySetId, directoryId);
     100    TestJob.test_execute(jobIdMatrix2);
     101   
    85102    // One-to-one mapping on assays and reporters
    86     int jobId2 = test_create_job(pluginConfigurationId2, experimentId, directoryId);
     103    int jobId2 = test_create_job(pluginConfigurationIdMatrix, experimentId, rootBioAssaySetId, directoryId);
    87104    TestJob.test_execute(jobId2);
    88105
    89106    // Merge assays
    90     int jobId3 = test_create_job(pluginConfigurationId2, experimentId, directoryId,
     107    int jobId3 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId,
    91108        new Parameter("mergeAssays", "1"));
    92109    TestJob.test_execute(jobId3);
    93110
    94111    // Offset positions
    95     int jobId4 = test_create_job(pluginConfigurationId2, experimentId, directoryId,
     112    int jobId4 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId,
    96113        new Parameter("offsetPositions", "1"));
    97114    TestJob.test_execute(jobId4);
    98115
    99116    // Offset positions and merge assays
    100     int jobId5 = test_create_job(pluginConfigurationId2, experimentId, directoryId,
     117    int jobId5 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId,
    101118        new Parameter("mergeAssays", "1"), new Parameter("offsetPositions", "1"));
    102119    TestJob.test_execute(jobId5);
    103120
    104121    // Create reporter list
    105     int jobId6 = test_create_job(pluginConfigurationId2, experimentId, directoryId,
     122    int jobId6 = test_create_job(pluginConfigurationId2, experimentId, rootBioAssaySetId, directoryId,
    106123        new Parameter("reporterList", "1"));
    107124    TestJob.test_execute(jobId6);
     
    118135      }
    119136    }
     137    TestExtraValueType.test_delete(aExtraValueId);
    120138    TestPluginConfiguration.test_delete(pluginConfigurationId);
    121139    TestPluginConfiguration.test_delete(pluginConfigurationId2);
     140    TestPluginConfiguration.test_delete(pluginConfigurationIdMatrix);
    122141    TestFormula.test_delete(formulaId);
    123142    TestFormula.test_delete(formulaChromosomeId);
    124143    TestFile.test_delete(fileId);
    125144    TestFile.test_delete(fileId2);
     145    TestFile.test_delete(fileIdMatrix);
    126146    TestDirectory.test_delete(directoryId, true);
    127147    TestReporter.test_delete();
     
    175195  }
    176196 
    177   static int test_create_job(int pluginConfigurationId, int experimentId, int directoryId, Parameter... parameters)
     197  static int test_create_job(int pluginConfigurationId, int experimentId, int bioAssaySetId, int directoryId, Parameter... parameters)
    178198  {
    179199    if (pluginConfigurationId == 0 || !TestUtil.hasPermission(Permission.CREATE, Item.JOB)) return 0;
     
    185205
    186206      Experiment e = Experiment.getById(dc, experimentId);
    187       BioAssaySet bioAssaySet = e.getBioAssaySets().iterate(dc).next();
     207      BioAssaySet bioAssaySet = BioAssaySet.getById(dc, bioAssaySetId);
    188208     
    189209      PluginConfiguration pc = PluginConfiguration.getById(dc, pluginConfigurationId);
  • trunk/src/test/TestBioAsssaySetExporter.java

    r4514 r4537  
    109109      TestExperiment.test_add_rawbioassay(experiment, rba2);
    110110      bas = TestExperiment.test_create_root_bioassayset_using_calculator(experiment, "medianfg", new int[] {rba1, rba2});
    111       TestExperiment.test_calculate_spotextravalues(bas, 0, 0, 0);
    112111     
    113112      test_exportBaseFile(bas, file, false, false);
  • trunk/src/test/TestExperiment.java

    r4514 r4537  
    108108   
    109109   
    110     int filterBasId = test_filter_bioassayset(rootBasId);
     110    int filterBasId = test_filter_bioassayset(rootBasId, 2.0f);
    111111    int basId = test_create_bioassayset(filterBasId);
    112112   
     
    115115    int stringExtraId = TestExtraValueType.test_create("test.string", Type.STRING, false);
    116116   
    117     int extraSpotId = test_calculate_spotextravalues(filterBasId, intExtraId, floatExtraId, stringExtraId);
     117    int extraSpotId = test_calculate_spotextravalues(filterBasId, true,
     118        intExtraId, floatExtraId, stringExtraId);
    118119    int extraPosId = test_calculate_positionextravalues(filterBasId, intExtraId, floatExtraId, stringExtraId);
    119120    // TODO
     
    932933  }
    933934
    934   static int test_filter_bioassayset(int bioAssaySetId)
     935  static int test_filter_bioassayset(int bioAssaySetId, float factor)
    935936  {
    936937    if (bioAssaySetId == 0) return 0;
     
    961962        )
    962963      );
    963       query.setParameter("factor", 2, Type.INT);
     964      query.setParameter("factor", factor, Type.FLOAT);
    964965     
    965966      FilterBatcher filterBatcher = bas.getFilterBatcher();
     
    996997  }
    997998
    998   static int test_calculate_spotextravalues(int bioAssaySetId, int intExtraId, int floatExtraId, int stringExtraId)
     999  static int test_calculate_spotextravalues(int bioAssaySetId, boolean createChild,
     1000      int intExtraId, int floatExtraId, int stringExtraId)
    9991001  {
    10001002    if (bioAssaySetId == 0) return 0;
     
    10061008      BioAssaySet source = BioAssaySet.getById(dc, bioAssaySetId);
    10071009     
    1008       Transformation t = source.newTransformation(null);
    1009       dc.saveItem(t);
    1010 
    1011       BioAssaySet bas = t.newProduct(null, null, true);
    1012       bas.setName("Extra spot values bioassayset");
    1013       dc.saveItem(bas);
     1010      BioAssaySet insertTo = source;
     1011      if (createChild)
     1012      {
     1013        Transformation t = source.newTransformation(null);
     1014        dc.saveItem(t);
     1015 
     1016        insertTo = t.newProduct(null, null, true);
     1017        insertTo.setName("Extra spot values bioassayset");
     1018        dc.saveItem(insertTo);
     1019      }
    10141020
    10151021      SpotExtraValueBatcher<Integer> intBatcher = null;
     
    10171023      {
    10181024        ExtraValueType intExtraValue = ExtraValueType.getById(dc, intExtraId);
    1019         intBatcher = bas.getSpotExtraValueBatcher(Integer.class, intExtraValue, null);
     1025        intBatcher = insertTo.getSpotExtraValueBatcher(Integer.class, intExtraValue, null);
    10201026      }
    10211027      SpotExtraValueBatcher<Float> floatBatcher = null;
     
    10231029      {
    10241030        ExtraValueType floatExtraValue = ExtraValueType.getById(dc, floatExtraId);
    1025         floatBatcher = bas.getSpotExtraValueBatcher(Float.class, floatExtraValue, null);
     1031        floatBatcher = insertTo.getSpotExtraValueBatcher(Float.class, floatExtraValue, null);
    10261032      }
    10271033      SpotExtraValueBatcher<String> stringBatcher = null;
     
    10291035      {
    10301036        ExtraValueType stringExtraValue = ExtraValueType.getById(dc, stringExtraId);
    1031         stringBatcher = bas.getSpotExtraValueBatcher(String.class, stringExtraValue, null);
     1037        stringBatcher = insertTo.getSpotExtraValueBatcher(String.class, stringExtraValue, null);
    10321038      }
    10331039     
     
    10641070
    10651071      dc.commit();
    1066       id = bas.getId();
    1067       dc = TestUtil.getDbControl();
    1068       dc.reattachItem(bas);
    1069       write_item(0, bas);
     1072      id = insertTo.getId();
     1073      dc = TestUtil.getDbControl();
     1074      dc.reattachItem(insertTo);
     1075      write_item(0, insertTo);
    10701076      write("--Calculate spot extra values OK ("+numSpots+" values inserted)");
    10711077
  • trunk/src/test/TestLowessNormalization.java

    r4514 r4537  
    5252  {
    5353    write("++Testing TestLowessNormalization");
    54     int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100);
     54    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100, 1.0f);
    5555
    5656    int formulaId = TestFormula.test_create(null, Formula.Type.INTENSITY_EXPRESSION,
  • trunk/src/test/TestMedianRatioNormalization.java

    r4514 r4537  
    5151  {
    5252    write("++Testing MedianRatioNormalization");
    53     int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100);
     53    int experimentId = TestAnalyzePluginUtil.test_createExperiment("data/test.rawdata.import.txt", 2, 100, 1.0f);
    5454    int formulaId = TestFormula.test_create(null, Formula.Type.INTENSITY_EXPRESSION,
    5555        "genepix", new String[] { "raw('ch1FgMedian')", "raw('ch2FgMedian')" }, false);
  • trunk/src/test/data/test.nullplugin.base

    r4232 r4537  
    11BASEfile
    22section plugin
    3 uniqueName  onk.lu.se/enell/wget
     3uniqueName  nullplugin-serial
    44versionNumber 1.0
    55name  Base1NullPlugin
  • trunk/www

    • Property svn:ignore deleted
  • trunk/www/admin/plugindefinitions/select_installation_type.jsp

    r4510 r4537  
    8787  </base:head>
    8888  <base:body onload="init()">
    89     <form name="installations" action="index.jsp" method="get" onsubmit="return false;">
     89    <form name="installations" action="index.jsp" method="post" onsubmit="return false;">
    9090    <input type="hidden" name="ID" value="<%=ID%>">
    9191    <input type="hidden" name="cmd" value="InstallationType">
  • trunk/www/admin/softwaretypes/view_softwaretype.jsp

    r4510 r4537  
    113113        onclick="newSoftware()"
    114114        title="New software&hellip;"
    115         tooltip="Create a new hardware of this type"
     115        tooltip="Create a new software of this type"
    116116        visible="<%=sc.hasPermission(Permission.CREATE, Item.SOFTWARE) && usePermission%>"
    117117      />
  • trunk/www/biomaterials/samples/list_samples.jsp

    r4510 r4537  
    634634                    image="add.png"
    635635                    onclick="<%="newExtract("+itemId+")"%>"
    636                     tooltip="Create new sample"
     636                    tooltip="Create new extract"
    637637                    visible="<%=mode.hasEditLink() && createExtractPermission && usePermission %>"
    638638                  />
  • trunk/www/common/columns/confirm_delete.jsp

    r4510 r4537  
    4848  </base:note>
    4949  <p>
    50   <form action="submit_preset.jsp" method="get" name="confirm">
     50  <form action="submit_preset.jsp" method="post" name="confirm">
    5151    <input type=hidden name="ID" value="<%=ID%>">
    5252    <input type=hidden name="cmd" value="Delete">
  • trunk/www/common/columns/save_preset.jsp

    r4510 r4537  
    8686<base:body onload="init()">
    8787  <p>
    88   <form name="preset" action="submit_preset.jsp" method="get" onsubmit="return validateForm();">
     88  <form name="preset" action="submit_preset.jsp" method="post" onsubmit="return validateForm();">
    8989  <input type="hidden" name="ID" value="<%=ID%>">
    9090  <input type="hidden" name="cmd" value="Save">
  • trunk/www/common/context/saveas.jsp

    r4510 r4537  
    7777<base:body onload="init()">
    7878  <p>
    79   <form name="preset" action="index.jsp" method="get" onsubmit="return validateForm();">
     79  <form name="preset" action="index.jsp" method="post" onsubmit="return validateForm();">
    8080  <input type=hidden name="ID" value="<%=ID%>">
    8181  <input type=hidden name="cmd" value="SaveCurrentContext">
  • trunk/www/common/import/no_fileformat.jsp

    r4510 r4537  
    104104  </base:head>
    105105  <base:body>
    106     <form name="import" action="index.jsp" method="get" onsubmit="return false;">
     106    <form name="import" action="index.jsp" method="post" onsubmit="return false;">
    107107    <input type="hidden" name="ID" value="<%=ID%>">
    108108    <input type="hidden" name="cmd" value="AutoDetect">
  • trunk/www/common/import/select_plugin.jsp

    r4510 r4537  
    212212  </base:head>
    213213  <base:body onload="init()">
    214     <form name="import" action="index.jsp" method="get" onsubmit="return false;">
     214    <form name="import" action="index.jsp" method="post" onsubmit="return false;">
    215215    <input type="hidden" name="ID" value="<%=ID%>">
    216216    <input type="hidden" name="cmd" value="RunPlugin">
  • trunk/www/common/plugin/finish_job.jsp

    r4510 r4537  
    106106  </base:head>
    107107  <base:body>
    108     <form name="plugin" action="index.jsp" method="get" onsubmit="return false;">
     108    <form name="plugin" action="index.jsp" method="post" onsubmit="return false;">
    109109    <input type="hidden" name="ID" value="<%=ID%>">
    110110    <input type="hidden" name="cmd" value="FinishNewJob">
  • trunk/www/common/plugin/select_plugin.jsp

    r4510 r4537  
    194194  </base:head>
    195195  <base:body onload="init()">
    196     <form name="plugin" action="index.jsp" method="get" onsubmit="return false;">
     196    <form name="plugin" action="index.jsp" method="post" onsubmit="return false;">
    197197    <input type="hidden" name="ID" value="<%=ID%>">
    198198    <input type="hidden" name="cmd" value="NewJob">
  • trunk/www/logout.jsp

    r4511 r4537  
    7979<base:body>
    8080  <br>
    81   <form action="logout.jsp" method="get" name="logout" onsubmit="return false;">
     81  <form action="logout.jsp" method="post" name="logout" onsubmit="return false;">
    8282    <input type="hidden" name="ID" value="<%=ID%>">
    8383    <input type="hidden" name="noconfirm" value="1">
  • trunk/www/plugins/net/sf/basedb/clients/web/plugins/simple_export.jsp

    r4511 r4537  
    251251  </base:head>
    252252  <base:body onload="init()">
    253     <form name="export" action="index.jsp" method="get" onsubmit="return false;">
     253    <form name="export" action="index.jsp" method="post" onsubmit="return false;">
    254254    <input type="hidden" name="ID" value="<%=ID%>">
    255255    <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">
  • trunk/www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp

    r4511 r4537  
    284284  </base:head>
    285285  <base:body onload="init()">
    286     <form name="extraValue" action="index.jsp" method="get" onsubmit="return false;">
     286    <form name="extraValue" action="index.jsp" method="post" onsubmit="return false;">
    287287    <input type="hidden" name="ID" value="<%=ID%>">
    288288    <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">
  • trunk/www/plugins/net/sf/basedb/plugins/jep_filter.jsp

    r4511 r4537  
    291291  </base:head>
    292292  <base:body onload="init()">
    293     <form name="filter" action="index.jsp" method="get" onsubmit="return false;">
     293    <form name="filter" action="index.jsp" method="post" onsubmit="return false;">
    294294    <input type="hidden" name="ID" value="<%=ID%>">
    295295    <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">
  • trunk/www/plugins/net/sf/basedb/plugins/jep_intensity_transformer.jsp

    r4511 r4537  
    165165  </base:head>
    166166  <base:body onload="init()">
    167     <form name="transformation" action="index.jsp" method="get" onsubmit="return false;">
     167    <form name="transformation" action="index.jsp" method="post" onsubmit="return false;">
    168168    <input type="hidden" name="ID" value="<%=ID%>">
    169169    <input type="hidden" name="requestId" value="<%=request.getParameter("requestId")%>">
  • trunk/www/views/experiments/overview/save_preset.jsp

    r4511 r4537  
    8585<base:body onload="init()">
    8686  <p>
    87   <form name="preset" action="index.jsp" method="get" onsubmit="return validateForm();">
     87  <form name="preset" action="index.jsp" method="post" onsubmit="return validateForm();">
    8888  <input type="hidden" name="ID" value="<%=ID%>">
    8989  <input type="hidden" name="cmd" value="Save">
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