Changeset 320

Timestamp:

02/27/10 20:02:04 (5 months ago)

Author:

martijn

Message:

Tweaked rdb.construct package for coming HMDB update

Location:

trunk/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct

Files:

• GdbConstruct.java (modified) (2 diffs)
• GdbConstructImpl3.java (modified) (8 diffs)

trunk/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/GdbConstruct.java

@@ -32 +32 @@
          * @return 1 if addition was successful, 0 otherwise. 
          */
-        public int addGene(Xref ref, String bpText); 
+        public int addGene(Xref ref);
 
         /**
@@ -67 +67 @@
         /**
          * Excecutes several SQL statements to create the tables and indexes in the database the given
-         * connection is connected to
-         * Note: Official GDB's are created by Alex Pico's script, not with this code.
-         * This is just here for testing purposes.
+         * connection is connected to.
          */
-        abstract public void createGdbTables(); 
+        abstract public void createGdbTables() throws IDMapperException;        
 
+        abstract public void commit() throws IDMapperException;
+        
+        abstract public void finalize() throws IDMapperException;
 }

trunk/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/GdbConstructImpl3.java

@@ -51 +51 @@
 
         /** {@inheritDoc} */
-        public int addGene(Xref ref, String bpText) 
+        public int addGene(Xref ref)
         {
                 //TODO: bpText is unused
@@ -62 +62 @@
                 } 
                 catch (SQLException e) 
-                { 
-//                      Logger.log.error("" + ref, e);
+                {
                         return 1;
                 }
@@ -79 +78 @@
                         pstAttr.executeUpdate();
                 } catch (SQLException e) {
-//                      Logger.log.error(attr + "\t" + val + "\t" + ref, e);
                         return 1;
                 }
@@ -97 +95 @@
                         pstLink.executeUpdate();
                 } 
-                catch (SQLException e)
-                {
-//                      Logger.log.error(left + "\t" + right , e);
+        catch (SQLException e) 
+                {
                         return 1;
                 }
@@ -177 +174 @@
          * Note: Official GDB's are created by AP, not with this code.
          * This is just here for testing purposes.
-         */
-        public void createGdbTables() 
+         * @throws IDMapperException 
+         */
+        public void createGdbTables() throws IDMapperException 
         {
 //              Logger.log.info("Info:  Creating tables");
@@ -184 +182 @@
                 {
                         Statement sh = con.createStatement();
-                        sh.execute("DROP TABLE info");
-                        sh.execute("DROP TABLE link");
-                        sh.execute("DROP TABLE datanode");
-                        sh.execute("DROP TABLE attribute");
-                } 
-                catch(SQLException e) 
-                {
-//                      Logger.log.error("Unable to drop gdb tables (ignoring): " + e.getMessage());
-                }
-
-                try
-                {
-                        Statement sh = con.createStatement();
+//                      sh.execute("DROP TABLE info");
+//                      sh.execute("DROP TABLE link");
+//                      sh.execute("DROP TABLE datanode");
+//                      sh.execute("DROP TABLE attribute");
+//                      sh.close();
+                        
+//                      sh = con.createStatement();
                         sh.execute(
                                         "CREATE TABLE                                   " +
@@ -222 +214 @@
                                         "               datanode                                                " +
                                         " (   id VARCHAR(50),                                   " +
-                                        "     code VARCHAR(50)                                  " +
+                                        "     code VARCHAR(50),                                 " +
                                         "     PRIMARY KEY (id, code)                    " +
                                         " )                                                                             ");
@@ -238 +230 @@
                 catch (SQLException e)
                 {
-//                      Logger.log.error("while creating gdb tables: " + e.getMessage(), e);
+                        throw new IDMapperException (e);
                 }
         }