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

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

Motivation

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)

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

Object-Relational Layer Design

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)

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

Overview of Implementation

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

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

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)

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)

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, … )

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

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

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 &

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.

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(); }

Status of Implementation

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.

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

Future Plans

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