1. Java Object-Relational Layer
GUS 3.0 Workshop
June 18-21, 2002

2. Agenda Motivation Overview of Design Overview of Implementation
Status of Implementation
Discussion of Future Plans

3. Motivation

4. Why another object layer?
Design of new Annotation Tool
prompted a review of the current method for interacting with the database from Java
current annotator interface queries with JDBC and writes XML which is parsed and processed using Perl ga-plugin
avoid having to update class files on client machines
particularly since interacting with development database
avoid having SQL generated on client machines
Long term goal of being able to serve generic objects to the public (for example using BioJava)

5. Options Considered SOAP Java Objects and CORBA
Java Objects and Java RMI
Supports dynamic class loading
Automatic garbage collection
Decided to use
Port to use CORBA fairly straightforward, if desired

6. Object-Relational Layer Design

7. Overview of Design Based on Perl Object-Relational Layer
Utility Classes
Objects mapped to tables in GUS 3.0
Code Generator
Relationships modeled as parent/child
Accessible using Java RMI
Remote Interface for the GUS Server
Implementation of the remote GUS Server
Client uses remote GUS Server to obtain GUS objects (by value)

8. Overview of Design (continued)
Erebus
Zeus
GUS Objects
(Serializable)
GUSdev
(GUS3.0)
Remote GUS Server …
Clients

9. Overview of Implementation

10. Overview of Implementation
Utility Classes
cbil.gus.Objects.GUS30.util
Code Generator GUS30::GUS_utils::JavaGenerator.pm
Remote Interfaces
RemoteGUSServer, RemoteGUSJDBCServer
Running remote GUSServer and Client access

11. Generated Subclasses of
cbil.gus.Objects.GUS30.util
GUSTableAttribute
GUSTable
GUSRow
Generated Subclasses of
GUSRow for each
table/view
GUSTableRelation
GUSJDBCServer
GUSObjectCache
SQLutils
GUSServer

12. Implementation: RemoteGUSServer
public String openConnection(String usr, String pswd)
throws RemoteException,GUSException;
Verifies username/password
Creates a GUSConnection, including an instance of GUSJDBCServer (connection to GUSdev)
Saves off some information about the connection
Returns a session id (String)
public GUSRow retrieveObject(String session, String pswd,
String owner, String tname, Integer pk)
throws RemoteException, GUSException, SQLException;
Verifies valid session and password
Queries database to retrieve requested row
Returns an instance of owner.tablename (eg. Core.Workflow)

13. Implementation: RemoteGUSServer
public GUSRow submitObject(String session,
String pswd, GUSRow obj)
throws RemoteException, GUSException, SQLException;
Verifies session and password
Submits object to database
Submits children to database
Returns updated object
public GUSRow createObject(String session, String pswd, String owner, String tname)
throws RemoteException, GUSException;
Verifies username/password
Returns a new instance of the specified class (owner.tname)

14. Implementation: RemoteGUSServer
public List getSessionHistory(String session, String pswd) throws RemoteException, GUSException;
Verifies session and password
Returns a List of transactions in this session
public void closeConnection(String session, String pswd) throws RemoteException, GUSException;
Closes GUSConnection
Etc. (getParent, getChildren, … )

15. Code Generation Execute command file: Calls generateGusJavaObjects.pl
cbil/gus/Objects/GUS30/CreateAllJavaObjects.cmd
should be executed from directory where want objects created
Calls generateGusJavaObjects.pl
…GUS30/bin/generateGusJavaObjects.pl --login GUSrw --database GUS30 --specialCases ./gus_special_cases
Same as generateGusPerlObjects.pl, but uses different code generation package

16. Code Generation (continued)
Uses GUS30::GUS_utils::JavaGenerator.pm
Creates java source files:
./<namespace>/<tablename>.java
./<namespace>/gen/<tablename>_gen.java
./<namespace>/gen/<tablename>_tbl.java
Compiles all generated code
currently assumes java is in your path
hand_edited code not ported to Java yet

17. Starting Remote GUS Server
// to generate stubs and skeletons
rmic -d /home/diskins/java_dev/GUS/java/ \
cbil.gus.Objects.GUS30.util.GUSServer
cbil.gus.Objects.GUS30.util.GUS_JDBC_Server
// start the rmiregistry
rmiregistry &
// to start the remote GUSServer - without a codebase ...
java \
-Djava.security.policy=/home/diskins/RMIServer/policy.txt \
-Djava.rmi.server.logCalls=true \
cbil.gus.Objects.GUS30.util.GUSServer \
>& GUSServer.log &

18. GUSServer registered with rmiregistry
public static void main(String[] args) {
try {
GUSServer server = new GUSServer();
String name = System.getProperty("gusservername", "GUSServer_1") ;
Naming.rebind(name, server);
System.out.println(name + " is bound in RMIRegistry and ready to serve."); }
catch ( Exception e ) {
System.err.println(e);
System.err.println("Usage: java [-Dgusservername=<name>] " +
"cbil.gus.Objects.GUS30.util.GUSServer");
System.exit(1); //force exit cause may be hanging RMI threads.

19. Client access to remote GUSServer
public static void main (String argv[]) {
...
try {
// Get a reference to the Remote GUS Server object...
System.out.println("Looking for remote GUS Server...");
String name = "rmi:///GUSServer_1"; //here assumes local machine...
RemoteGUSServer gi = (RemoteGUSServer)Naming.lookup(name);
System.out.println("Obtained reference to remote GUS Server");
// Open a session with the remote GUS Server Object...
String session = gi.openConnection(user, password);
System.out.println("New Session is : " + session + "\n"); …
}catch (Exception e) {
System.err.println(e);
e.printStackTrace(); }

20. Status of Implementation

21. What “works” now Code Generation (except hand edited)
RMI Server accepting connections
Create new objects (subclasses of GUSRow)
Set attribute values
Set / Get parent
Set / Get child (ren)
Simple submits: insert, update, delete
Deep submits not fully tested yet
Basic error checking
Username/password, valid attributes, etc.

22. What still needs to be done
More error checking/handling
Read/write permissions (config file initialization)
Port “Hand edited” classes to Java
Evidence and Similarity handling
Test, test, test

23. Future Plans

24. Discussion of Possible Plans
GUSApplication for Java
May help with submits
Could also just be handled by GUSServer
CBIL effort
BioJava Wrappers to GUS Java Objects
Would aid in java interface implementations
Could be served to the public
Sanger (or joint) effort ?
Sanger – BioJava expertise
CBIL – Schema and GUS Java object expertise
Perhaps start with educated estimate of resource requirements