[Biojava-l] Logging in BJ3

[Mark Schreiber]

Hi -

I would like to strongly advocate the liberal and extensive use of
Logging in BioJava3.  The lack of this plagued us (me at least) during
bug fixes in previous versions of BioJava.  The default Java logging
API is very flexible and easily meets our needs. It's also not too
much effort for developers to put in place (you know you use
System.println() all over the place anyway).

The following is an example snippet using logging that would certainly
help debugging.  With the standard logging setup only the severe
statement would appear on the terminal. We could also provide config
files that show lower levels of logging so that people can easily
generate detailed logs to accompany bug reports.  If we want to be
really tricky we could even use a MemoryLogger that has a rotating
buffer of log statements that could spit out with a stack trace so you
could just submit the stack trace and the activity log all in one go
and we can get an idea of what was going on at the time.

The example below also shows what to do to avoid a major performance
hit during logging. The marked "expensive logging operation" pretends
to get config information by getting it from a database. One might
expect this to take time while the db connects etc and could produce
quite a long String of information. To save time when logging is not
set to the CONFIG level the if statement is able to skip this costly
step.

I know from experience we will definitely get the most value from this
in the IO parsers and ThingBuilders.

Any thoughts?

- Mark



    private Logger logger = Logger.getLogger("org.biojava.MyClass");

    public Object generateObject(String argument){
         logger.entering(""+getClass(), "generateObject", argument);

         //expensive logging operation
         if (logger.isLoggable( Level.CONFIG )) {
            logger.config("DB config: "+ getDBConfigInfo());
         }

         Object obj = null;
         try{

            //do some stuff
            logger.fine("doing stuff");
            obj = new Object();

         }catch(Exception ex){
             logger.severe("Failed to do stuff");
             logger.throwing(""+getClass(), "generateObject", ex);
         }

         logger.exiting(""+getClass(), "generateObject", obj);
         return obj;
    }