Changeset 317 for trunk/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java

Timestamp:

02/25/10 20:57:40 (2 years ago)

Author:

martijn

Message:

Refactoring dead code:
Removed all methods pertaining to constructing Derby databases
to a separate package (org.bridgedb.rdb.construct). Also
factored out common code between SimpleGdbImpl?2/3 into
SimpleGdbImplCommon?

Files:

• trunk/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java (modified) (5 diffs)

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

@@ -17 +17 @@
 package org.bridgedb.rdb;
 
+import java.io.File;
+import java.io.IOException;
 import java.sql.Connection;
 import java.sql.DriverManager;
@@ -22 +24 @@
 import java.util.Collection;
 import java.util.Map;
+import java.util.Properties;
 import java.util.Set;
 
@@ -53 +56 @@
                 public IDMapper connect(String location) throws IDMapperException 
                 {
-                        return SimpleGdbFactory.createInstance(location, new DataDerby(), 0);
+                        try
+                        {
+                                String url = "jdbc:derby:jar:(" + location + ")database";
+                                Connection con = DriverManager.getConnection(url);
+                                return SimpleGdbFactory.createInstance(location, con);
+                        }
+                        catch (SQLException ex)
+                        {
+                                throw new IDMapperException(ex);
+                        }
                 }
         }
@@ -67 +79 @@
                         try
                         {
-                                Connection con = DriverManager.getConnection("jdbc:" + location);
-                        
-                                return SimpleGdbFactory.createInstance(location, con, 0);
+                                String url = "jdbc:" + location;
+                                Connection con = DriverManager.getConnection(url);
+                                return SimpleGdbFactory.createInstance(location, con);
                         }
                         catch (SQLException ex)
@@ -86 +98 @@
                 public IDMapper connect(String location) throws IDMapperException 
                 {
-                        //TODO: make port and host configurable
-                        DBConnectorDerbyServer.init ("wikipathways.org", 1527);
-                        return SimpleGdbFactory.createInstance(location, new DBConnectorDerbyServer(), 0);
+                        try
+                        {
+                    Map<String, String> args = 
+                        InternalUtils.parseLocation(location, "host", "port");
+
+                    if (!args.containsKey("BASE")) 
+                        throw new IllegalArgumentException("Expected species name in connection string: " + location);
+
+                    String host = args.containsKey("host") ? args.get("host") : "wikipathways.org";
+                    String port = args.containsKey("port") ? args.get("port") : "1527";
+                    
+                                Class.forName("org.apache.derby.jdbc.ClientDriver");
+                                Properties sysprop = System.getProperties();
+                                sysprop.setProperty("derby.storage.tempDirectory", System.getProperty("java.io.tmpdir"));
+                                sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString());
+                                
+                                String url = "jdbc:derby://" + host + ":" + port + "/" + args.get("BASE");
+                                Connection con = DriverManager.getConnection(url);
+                                return SimpleGdbFactory.createInstance(location, con);
+                        }
+                        catch (SQLException f)
+                        {
+                                throw new IDMapperException (f);
+                        }
+                        catch (IOException e)
+                        {
+                                throw new IDMapperException (e);
+                        }
+                        catch (ClassNotFoundException e)
+                        {
+                                throw new IDMapperException (e);
+                        }
                 }
         }