[Bioperl-pipeline] Re: java adaptors for biopipe

[Elia Stupka]

> what adaptors do you want for the biopipe? Can you give me a list, or
> you want adaptor for each table?

The best thing is if you look at the codebase in bioperl-pipeline, to
understand the object layer. Also you should talk to Frans because he has
been playing with the idea of a PipelineManager in java for a while.

Not all tables need their own classes, because some are simply
relationships tables, as you can see from the ER diagram on the INSTALL
section of www.biopipe.org

Also, the main classes are just classes, i.e. "business objects", the
adaptors are only used for the SQL classes that let the business objects
be stored and fetched from the database.

A general (simplified) rule is that you wouldn't want classes for
tablename_tablename tables such as analysis_iohandler, because they simply
represent relationships

> +-----------------------+
> | analysis              |
> | analysis_iohandler    |
> | argument              |
> | completed_jobs        |
> | datahandler           |
> | dbadaptor             |
> | input                 |
> | iohandler             |
> | iohandler_map         |
> | job                   |
> | new_input             |
> | new_input_ioh         |
> | node                  |
> | node_group            |
> | output                |
> | rule                  |
> | streamadaptor         |
> +-----------------------+
> 

Elia

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