[Biojava-dev] maven progress

[Michael Heuer]

Andreas Prlic wrote:

> >> The new SVN location is emerging here:
> >>
> >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava
> >
> > That seems like an odd place for it, at the same level as branches, tags,
> > and trunk?
> >
> > If you've branched for 1.7 and called for the freeze on trunk, I don't see
> > any reason not to do this work on trunk.
>
> ok. makes sense.  It is easy to flip locations around in svn..  I can
> move the old trunk  e.g. to a tag folder for archive purposes and make
> what is called biojava right now the future trunk. (in svn this moves
> or copy operations are cheap)  For the moment things are not
> stabilized yet and I will do this once things are there...

That's cool.  I wanted to check in some preliminary fastq stuff and wasn't
sure where it should go.  I'm in the biojava3 branch for now, and will
move to the right place once things settle.


> At the moment I am chasing an "interesting" problem. When I run the
> junit tests on the new core module in eclipse, they run fine.   When I
> do the same via a mvn test I get several issues like the one below.
> Anybody got an idea?
>
> -------------------------------------------------------------------------------
> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest
> -------------------------------------------------------------------------------
> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036
> sec <<< FAILURE!
> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest)
>  Time elapsed: 0.011 sec  <<< ERROR!
> java.lang.AssertionError: firePreChangeEvent must be called in a
> synchronized block locking the ChangeSupport
> 	at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281)
> 	at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299)
> 	at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297)
> 	at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173)
> 	at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297)

I've always disliked the change stuff, how about get rid of it all and
make everything immutable?  ;)

   michael