Changeset 4167

Timestamp:

Mar 3, 2008, 9:20:28 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #941: SQLException when exporting "merged on reporters" with BioAssaySet? exporter on Postgres
References #939: BioAssaySetExporter? doesn't export BASEfiles for multiple array designs correctly

File:

• branches/2.6-stable/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (5 diffs)

branches/2.6-stable/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -72 +72 @@
 import net.sf.basedb.core.query.JoinType;
 import net.sf.basedb.core.query.Orders;
-import net.sf.basedb.core.query.Select;
 import net.sf.basedb.core.query.Selects;
 import net.sf.basedb.core.query.SqlResult;
@@ -318 +317 @@
       query.select(Selects.expression(qi.getExpression(dc, bas, mergeReporters), qi.getQueryAlias()));
     }
-
-    if (mergeReporters)
-    {
-      QueryItem qi = qis.get("rep.id");
-      Select rep = Selects.expression(qi.getExpression(dc, bas, mergeReporters), qi.getQueryAlias());
-      if (!reporterFields.contains(qi.getExportName()))
-      {
-        query.select(rep);
-      }
-      query.group(Dynamic.column(VirtualColumn.COLUMN));
-      query.group(Expressions.selected(rep));
-    }
-    
+  
     checkInterrupted();
     long count = getBaseFileSpotSectionCount(dc, bas.getSpotData(), mergeReporters);
     checkInterrupted();
-    exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, bas.getBioAssays().list(dc), qis, count);
+    exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, bas.getBioAssays().list(dc), qis, count, mergeReporters);
     out.flush();
   }
@@ -458 +445 @@
       }
 
-      if (mergeReporters)
-      {
-        QueryItem qi = qis.get("rep.id");
-        Select rep = Selects.expression(qi.getExpression(dc, bas, mergeReporters), qi.getQueryAlias());
-        if (!reporterFields.contains(qi.getExportName()))
-        {
-          query.select(rep);
-        }
-        query.group(rep.getExpression());
-      }
-
       checkInterrupted();
       long count = getBaseFileSpotSectionCount(dc, ba.getSpotData(), mergeReporters);
-      exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, Collections.singletonList(ba), qis, count);
+      exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, Collections.singletonList(ba), qis, count, mergeReporters);
       
       out.println();
@@ -480 +456 @@
 
   private void exportBaseFileSectionSpots(PrintWriter out, DbControl dc, BioAssaySet bas, DynamicSpotQuery query,
-    List<String> reporterFields, List<String> spotFields, List<BioAssay> assays, Map<String, QueryItem> qi, long count)
+    List<String> reporterFields, List<String> spotFields, List<BioAssay> assays, Map<String, QueryItem> qi, 
+    long count, boolean mergeOnReporters)
     throws SQLException
   {
@@ -516 +493 @@
     }
     
-    query.select(Selects.expression(Dynamic.column(VirtualColumn.POSITION), "_position"));
-    query.select(Selects.expression(Dynamic.column(VirtualColumn.COLUMN), "_column"));
-    query.order(Orders.asc(Dynamic.column(VirtualColumn.POSITION)));
-    query.order(Orders.asc(Dynamic.column(VirtualColumn.COLUMN)));
+    Expression posExpression = null;
+    Expression colExpression = null;
+    if (mergeOnReporters)
+    {
+      posExpression = Dynamic.column(VirtualTable.POSITION, VirtualColumn.REPORTER_ID);
+      colExpression = Dynamic.column(VirtualColumn.COLUMN);
+      query.group(colExpression);
+      query.group(posExpression);
+    }
+    else
+    {
+      posExpression = Dynamic.column(VirtualColumn.POSITION);
+      colExpression = Dynamic.column(VirtualColumn.COLUMN);
+    }
+    query.select(Selects.expression(posExpression, "_position"));
+    query.select(Selects.expression(colExpression, "_column"));
+    query.order(Orders.asc(posExpression));
+    query.order(Orders.asc(colExpression));
     
     checkInterrupted();