Changeset 4592


Ignore:
Timestamp:
Oct 20, 2008, 11:08:06 AM (13 years ago)
Author:
Nicklas Nordborg
Message:

References #1150: Incorrect mapping of BASE1/BASE2 differences by Base1PluginExecuter

Tested and works with the test programs. Should be tested with more BASE1 plug-ins.

Location:
branches/2.8-stable/src
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • branches/2.8-stable/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

    r4531 r4592  
    911911      names.put(f.getName(), "frm."+f.getId());
    912912    }
    913    
    914     names.put("lastUpdate", "rep.lastUpdate");
    915     names.put("geneName", "rep.name");
    916     names.put("position", "rep.position");
    917     names.put("reporter", "rep.id");
    918     names.put("reporterId", "rep.externalId");
    919     names.put("geneSymbol", "rep.symbol");
    920    
    921     names.put("rawPosition", "raw.position");
    922     names.put("block", "raw.block");
    923     names.put("numCol", "raw.col");
    924     names.put("numRow", "raw.row");
    925     names.put("x", "raw.x");
    926     names.put("y", "raw.y");
    927    
     913
    928914    for (ExtraValue ev : bas.getExtraValues().list(dc))
    929915    {
  • branches/2.8-stable/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

    r4531 r4592  
    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));
  • branches/2.8-stable/src/test/TestBase1PluginExecuter.java

    r4581 r4592  
    7272    int formulaChromosomeId = TestFormula.test_create("chromosome",
    7373        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('chromosome')" }, false);
     74    int posFormulaId = TestFormula.test_create("position",
     75        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "pos()" }, false);
     76    int reporterFormulaId = TestFormula.test_create("reporter",
     77        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('id')" }, false);
     78    int externalIdFormulaId = TestFormula.test_create("reporterId",
     79        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('externalId')" }, false);
    7480   
    7581    int fileId = TestFile.test_create("data/test.nullplugin.base", false, false);
     
    143149    TestFormula.test_delete(formulaId);
    144150    TestFormula.test_delete(formulaChromosomeId);
     151    TestFormula.test_delete(posFormulaId);
     152    TestFormula.test_delete(reporterFormulaId);
     153    TestFormula.test_delete(externalIdFormulaId);
    145154    TestFile.test_delete(fileId);
    146155    TestFile.test_delete(fileId2);
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