This error appears when reverse engineering (trying to generate Java5 EJB3 code) a mysql database:
java.lang.NullPointerException
at org.hibernate.mapping.ForeignKey.alignColumns(ForeignKey.java:77)
at org.hibernate.mapping.ForeignKey.alignColumns(ForeignKey.java:73)
at org.hibernate.cfg.Configuration.secondPassCompileForeignKeys(Configuration.java:1263)
at org.hibernate.cfg.JDBCMetaDataConfiguration.secondPassCompileForeignKeys(JDBCMetaDataConfiguration.java:33)
at org.hibernate.cfg.Configuration.secondPassCompile(Configuration.java:1170)
at org.hibernate.cfg.Configuration.buildMappings(Configuration.java:1115)
at org.hibernate.eclipse.launch.CodeGenerationLaunchDelegate$2.execute(CodeGenerationLaunchDelegate.java:318)
at org.hibernate.console.execution.DefaultExecutionContext.execute(DefaultExecutionContext.java:64)
at org.hibernate.console.ConsoleConfiguration.execute(ConsoleConfiguration.java:94)
at org.hibernate.eclipse.launch.CodeGenerationLaunchDelegate.buildConfiguration(CodeGenerationLaunchDelegate.java:285)
at org.hibernate.eclipse.launch.CodeGenerationLaunchDelegate.runExporters(CodeGenerationLaunchDelegate.java:218)
at org.hibernate.eclipse.launch.CodeGenerationLaunchDelegate.launch(CodeGenerationLaunchDelegate.java:138)
at org.eclipse.debug.internal.core.LaunchConfiguration.launch(LaunchConfiguration.java:853)
at org.eclipse.debug.internal.core.LaunchConfiguration.launch(LaunchConfiguration.java:703)
at org.eclipse.debug.internal.ui.DebugUIPlugin.buildAndLaunch(DebugUIPlugin.java:866)
at org.eclipse.debug.internal.ui.DebugUIPlugin$8.run(DebugUIPlugin.java:1069)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)

You will find herebelow the sql schema, to import into a mysql 5.0 database. I used mysql --default-character-set=utf8 to import it.

The error does not happen if the last line of the schema (adding a foreign key) is removed.

Using eclipse Platform Version: 3.5.1 Build id: M20090917-0800 on debian etch, Hibernate Tools 3.2.4.v200909151014R-H192-GA.

Thanks for any help.

----
DROP TABLE IF EXISTS Catégorie;
CREATE TABLE Catégorie
(
ID Int8
);

DROP TABLE IF EXISTS Transaction;
CREATE TABLE Transaction
(
Compte_positif Int8
);
alter table Catégorie ADD INDEX(ID);
alter table Transaction add constraint youpee foreign key (Compte_positif) references Catégorie(ID);

report in jira please

Done. https://jira.jboss.org/jira/browse/JBIDE-5461

I am a newbie on hibernate. Could someone tell me whether the patch is incorporated in the official release? I have the hibernate-3.6.0 final distribution from sourceforge and it doesn't seem to contain the patch. I would like to know how to get the official patch for this bug.

No, they didn't upply the patch.
Actually the class was not changes since hibernate 3.2