Changeset 4605


Ignore:
Timestamp:
Oct 27, 2008, 10:00:35 AM (13 years ago)
Author:
Nicklas Nordborg
Message:

Merged patch release 2.8.4 to the trunk

Location:
trunk
Files:
8 edited

Legend:

Unmodified
Added
Removed
  • trunk/credits.txt

    r4585 r4605  
    2626USA.
    2727
    28 The current BASE team is (at BASE 2.8.3 release)
     28The current BASE team is (at BASE 2.8.4 release)
    2929
    3030Jari Häkkinen
  • trunk/src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java

    r4544 r4605  
    7070    Formatter<Number> numberFormatter = FormatterFactory.getNumberFormatter(sc);
    7171    Formatter<Number> intFormatter = FormatterFactory.getIntFormatter(sc);
    72     columns.add(new TableColumn("POSITION", "POSITION", null, Type.INT,
     72    columns.add(new TableColumn("POSITION", "POSITION", "pos()", Type.INT,
    7373      "Position", "Spot position", "always", true, true, true,
    7474      Formula.AverageMethod.NONE, intFormatter));
     
    130130    Formatter<String> stringFormatter = FormatterFactory.getStringFormatter(sc);
    131131    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
     132    columns.add(new TableColumn(idPrefix + "id", propertyPrefix+"id", "rep('id')",
     133      Type.INT, titlePrefix + "Internal ID", "Reporter internal ID", "auto", true, true, true,
     134      Formula.AverageMethod.NONE, null));
    132135    columns.add(new TableColumn(idPrefix + "name", propertyPrefix+"name", "rep('name')",
    133136      Type.STRING, titlePrefix + "Name", "Reporter name", "auto", true, true, true,
    134137      Formula.AverageMethod.NONE, stringFormatter));
    135138    columns.add(new TableColumn(idPrefix + "externalId", propertyPrefix+"externalId", "rep('externalId')",
    136       Type.STRING, titlePrefix + "ID", "Reporter ID", "auto", true, true, true,
     139      Type.STRING, titlePrefix + "External ID", "Reporter ID", "auto", true, true, true,
    137140      Formula.AverageMethod.NONE, stringFormatter));
    138141    columns.add(new TableColumn(idPrefix + "symbol", propertyPrefix+"symbol", "rep('symbol')",
  • trunk/src/core/net/sf/basedb/core/BasicItem.java

    r4527 r4605  
    221221  {
    222222    org.hibernate.Session session = getDbControl().getHibernateSession();
    223     org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, "COUNT_ANYTOANY_TO");
     223    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session,
     224      "COUNT_USED_ANYTOANY_TO");
    224225    /*
    225226      SELECT count(*)
  • trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

    r4513 r4605  
    868868      super.end(success);
    869869      ffp = null;
    870       mappers.clear();
    871       itemCache.clear();
     870      if (mappers != null) mappers.clear();
     871      if (itemCache != null) itemCache.clear();
    872872    }
    873873  }
  • trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

    r4537 r4605  
    909909      names.put(f.getName(), "frm."+f.getId());
    910910    }
    911    
    912     names.put("lastUpdate", "rep.lastUpdate");
    913     names.put("geneName", "rep.name");
    914     names.put("position", "rep.position");
    915     names.put("reporter", "rep.id");
    916     names.put("reporterId", "rep.externalId");
    917     names.put("geneSymbol", "rep.symbol");
    918    
    919     names.put("rawPosition", "raw.position");
    920     names.put("block", "raw.block");
    921     names.put("numCol", "raw.col");
    922     names.put("numRow", "raw.row");
    923     names.put("x", "raw.x");
    924     names.put("y", "raw.y");
    925    
     911
    926912    for (ExtraValue ev : bas.getExtraValues().list(dc))
    927913    {
  • trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

    r4537 r4605  
    10021002    items.add(new QueryItem("rep.position", "Position", "position", "pos()", Formula.AverageMethod.NONE));
    10031003    items.add(new QueryItem("rep.name", "Reporter Name", "name", "rep('name')", Formula.AverageMethod.MAX));
    1004     items.add(new QueryItem("rep.externalId", "Reporter ID", "reporterId", "rep('externalId')", Formula.AverageMethod.MAX));
     1004    items.add(new QueryItem("rep.externalId", "External ID", "externalId", "rep('externalId')", Formula.AverageMethod.MAX));
    10051005    items.add(new QueryItem("rep.symbol", "Gene symbol", "symbol", "rep('symbol')", Formula.AverageMethod.MAX));
    10061006    items.add(new QueryItem("rep.description", "Description", "description", "rep('description')", Formula.AverageMethod.MAX));
  • trunk/src/test/TestBase1PluginExecuter.java

    r4585 r4605  
    7070    int formulaChromosomeId = TestFormula.test_create("chromosome",
    7171        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('chromosome')" }, false);
     72    int posFormulaId = TestFormula.test_create("position",
     73        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "pos()" }, false);
     74    int reporterFormulaId = TestFormula.test_create("reporter",
     75        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('id')" }, false);
     76    int externalIdFormulaId = TestFormula.test_create("reporterId",
     77        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('externalId')" }, false);
    7278   
    7379    int fileId = TestFile.test_create("data/test.nullplugin.base", false, false);
     
    141147    TestFormula.test_delete(formulaId);
    142148    TestFormula.test_delete(formulaChromosomeId);
     149    TestFormula.test_delete(posFormulaId);
     150    TestFormula.test_delete(reporterFormulaId);
     151    TestFormula.test_delete(externalIdFormulaId);
    143152    TestFile.test_delete(fileId);
    144153    TestFile.test_delete(fileId2);
  • trunk/www/common/expression_builder.jsp

    r4510 r4605  
    263263      return channel;
    264264    }
    265    
     265    function pos()
     266    {
     267      return Math.random() * 100;
     268    }
    266269    function rep(property)
    267270    {
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