I've currently trying to generate classes based on my existing Postgres DB using JOOQ. In my JOOQ .xml config I have left out any inputSchema tags so that JOOQ generates all the schemas it finds:
<schemata>
<schema>
</schema>
</schemata>
You can use the <excludes>
configuration as documented here:
http://www.jooq.org/doc/latest/manual/code-generation/codegen-configuration
<includes>.*</includes>
<excludes>
(?i:information_schema\..*) # I'm using (?i: ... ) for case-insensitivity here...
</excludes>
Both <includes>
and <excludes>
take Java regular expressions as arguments, which make matching unwanted schemas relatively easy.