Changeset 542 for trunk

Timestamp:

08/26/11 15:49:49 (9 months ago)

Author:

thomas

Message:

added XrefIterator? interface and implemented for IDMapperRdb

Location:

trunk

Files:

• org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java (modified) (4 diffs)
• org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java (modified) (2 diffs)
• org.bridgedb/src/org/bridgedb/XrefIterator.java (added)

trunk/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java

@@ -19 +19 @@
 import java.io.File;
 import java.io.IOException;
-import java.sql.Connection;
-import java.sql.DriverManager;
-import java.sql.SQLException;
 import java.util.Collection;
 import java.util.Map;
@@ -33 +30 @@
 import org.bridgedb.IDMapperException;
 import org.bridgedb.Xref;
+import org.bridgedb.XrefIterator;
 import org.bridgedb.impl.InternalUtils;
 
@@ -39 +37 @@
  * such as looking up cross-references and backpage text.
  */
-public abstract class IDMapperRdb implements IDMapper, AttributeMapper
+public abstract class IDMapperRdb implements IDMapper, AttributeMapper, XrefIterator
 {
         static
@@ -125 +123 @@
         {
                 return InternalUtils.mapMultiFromSingle(this, srcXrefs, tgtDataSources);
-        }       
+        }
 }

trunk/org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java

@@ -77 +77 @@
                         "SELECT id, code, attrvalue FROM attribute WHERE " +
                         "attrname = ? AND LOWER(ID) LIKE ?"
+                );
+        final SimpleGdb.QueryLifeCycle qAllXrefs = new SimpleGdb.QueryLifeCycle(
+                        "SELECT id, code FROM datanode"
+                );
+        final SimpleGdb.QueryLifeCycle qAllXrefsByDatasource = new SimpleGdb.QueryLifeCycle(
+                        "SELECT id, code FROM datanode WHERE code = ?"
                 );
 
@@ -375 +381 @@
         }
 
+        @Override
+        public Iterable<Xref> getIterator() throws IDMapperException {
+                Set<Xref> xrefs = new HashSet<Xref>();
+                final QueryLifeCycle pst = qAllXrefs;
+                synchronized (pst) { 
+                try
+                {
+                        pst.init();
+                        ResultSet rs = pst.executeQuery();
+                        while (rs.next())
+                        {
+                                xrefs.add(new Xref(rs.getString(1), DataSource.getBySystemCode(rs.getString(2))));
+                        }
+                }
+                catch (SQLException ignore)
+                {
+                        throw new IDMapperException(ignore);
+                }
+                        finally {pst.cleanup(); }
+                return xrefs;
+                }               
+        }
+        
+        @Override
+        public Iterable<Xref> getIterator(DataSource ds) throws IDMapperException {
+                Set<Xref> xrefs = new HashSet<Xref>();
+                final QueryLifeCycle pst = qAllXrefsByDatasource;
+                synchronized (pst) { 
+                try
+                {
+                        pst.init();
+                        pst.setString(1, ds.getSystemCode());
+                        ResultSet rs = pst.executeQuery();
+                        while (rs.next())
+                        {
+                                xrefs.add(new Xref(rs.getString(1), ds));
+                        }
+                }
+                catch (SQLException ignore)
+                {
+                        throw new IDMapperException(ignore);
+                }
+                        finally {pst.cleanup(); }
+                return xrefs;
+                }
+        }
 }