Changeset 4592

Timestamp:

Oct 20, 2008, 11:08:06 AM (15 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:

• plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (1 diff)
• plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (1 diff)
• test/TestBase1PluginExecuter.java (modified) (2 diffs)

branches/2.8-stable/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -911 +911 @@
       names.put(f.getName(), "frm."+f.getId());
     }
-    
-    names.put("lastUpdate", "rep.lastUpdate");
-    names.put("geneName", "rep.name");
-    names.put("position", "rep.position");
-    names.put("reporter", "rep.id");
-    names.put("reporterId", "rep.externalId");
-    names.put("geneSymbol", "rep.symbol");
-    
-    names.put("rawPosition", "raw.position");
-    names.put("block", "raw.block");
-    names.put("numCol", "raw.col");
-    names.put("numRow", "raw.row");
-    names.put("x", "raw.x");
-    names.put("y", "raw.y");
-    
+
     for (ExtraValue ev : bas.getExtraValues().list(dc))
     {

branches/2.8-stable/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -1002 +1002 @@
     items.add(new QueryItem("rep.position", "Position", "position", "pos()", Formula.AverageMethod.NONE));
     items.add(new QueryItem("rep.name", "Reporter Name", "name", "rep('name')", Formula.AverageMethod.MAX));
-    items.add(new QueryItem("rep.externalId", "Reporter ID", "reporterId", "rep('externalId')", Formula.AverageMethod.MAX));
+    items.add(new QueryItem("rep.externalId", "External ID", "externalId", "rep('externalId')", Formula.AverageMethod.MAX));
     items.add(new QueryItem("rep.symbol", "Gene symbol", "symbol", "rep('symbol')", Formula.AverageMethod.MAX));
     items.add(new QueryItem("rep.description", "Description", "description", "rep('description')", Formula.AverageMethod.MAX));

branches/2.8-stable/src/test/TestBase1PluginExecuter.java

@@ -72 +72 @@
     int formulaChromosomeId = TestFormula.test_create("chromosome", 
         Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('chromosome')" }, false);
+    int posFormulaId = TestFormula.test_create("position",
+        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "pos()" }, false);
+    int reporterFormulaId = TestFormula.test_create("reporter",
+        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('id')" }, false);
+    int externalIdFormulaId = TestFormula.test_create("reporterId",
+        Formula.Type.COLUMN_EXPRESSION, "genepix", new String[] { "rep('externalId')" }, false);
     
     int fileId = TestFile.test_create("data/test.nullplugin.base", false, false);
@@ -143 +149 @@
     TestFormula.test_delete(formulaId);
     TestFormula.test_delete(formulaChromosomeId);
+    TestFormula.test_delete(posFormulaId);
+    TestFormula.test_delete(reporterFormulaId);
+    TestFormula.test_delete(externalIdFormulaId);
     TestFile.test_delete(fileId);
     TestFile.test_delete(fileId2);