Changeset 4605

Timestamp:

Oct 27, 2008, 10:00:35 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 2.8.4 to the trunk

Location:

trunk

Files:

• credits.txt (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/BasicItem.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (1 diff)
• src/test/TestBase1PluginExecuter.java (modified) (2 diffs)
• www/common/expression_builder.jsp (modified) (1 diff)

trunk/credits.txt

@@ -26 +26 @@
 USA.
 
-The current BASE team is (at BASE 2.8.3 release)
+The current BASE team is (at BASE 2.8.4 release)
 
 Jari Häkkinen

trunk/src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java

@@ -70 +70 @@
     Formatter<Number> numberFormatter = FormatterFactory.getNumberFormatter(sc);
     Formatter<Number> intFormatter = FormatterFactory.getIntFormatter(sc);
-    columns.add(new TableColumn("POSITION", "POSITION", null, Type.INT, 
+    columns.add(new TableColumn("POSITION", "POSITION", "pos()", Type.INT, 
       "Position", "Spot position", "always", true, true, true, 
       Formula.AverageMethod.NONE, intFormatter));
@@ -130 +130 @@
     Formatter<String> stringFormatter = FormatterFactory.getStringFormatter(sc);
     Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
+    columns.add(new TableColumn(idPrefix + "id", propertyPrefix+"id", "rep('id')", 
+      Type.INT, titlePrefix + "Internal ID", "Reporter internal ID", "auto", true, true, true,
+      Formula.AverageMethod.NONE, null));
     columns.add(new TableColumn(idPrefix + "name", propertyPrefix+"name", "rep('name')", 
       Type.STRING, titlePrefix + "Name", "Reporter name", "auto", true, true, true, 
       Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "externalId", propertyPrefix+"externalId", "rep('externalId')", 
-      Type.STRING, titlePrefix + "ID", "Reporter ID", "auto", true, true, true, 
+      Type.STRING, titlePrefix + "External ID", "Reporter ID", "auto", true, true, true, 
       Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "symbol", propertyPrefix+"symbol", "rep('symbol')", 

trunk/src/core/net/sf/basedb/core/BasicItem.java

@@ -221 +221 @@
   {
     org.hibernate.Session session = getDbControl().getHibernateSession();
-    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, "COUNT_ANYTOANY_TO");
+    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+      "COUNT_USED_ANYTOANY_TO");
     /*
       SELECT count(*)

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

@@ -868 +868 @@
       super.end(success);
       ffp = null;
-      mappers.clear();
-      itemCache.clear();
+      if (mappers != null) mappers.clear();
+      if (itemCache != null) itemCache.clear();
     }
   }

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

@@ -909 +909 @@
       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))
     {

trunk/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));

trunk/src/test/TestBase1PluginExecuter.java

@@ -70 +70 @@
     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);
@@ -141 +147 @@
     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);

trunk/www/common/expression_builder.jsp

@@ -263 +263 @@
       return channel;
     }
-    
+    function pos()
+    {
+      return Math.random() * 100;
+    }
     function rep(property)
     {