[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/gamexml GAMEAdapter.java,1.137,1.138

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gamexml
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2550/src/java/apollo/dataadapter/gamexml

Modified Files:
	GAMEAdapter.java 
Log Message:
annotation change events that were id updates were getting converted
to delete & add transaction in transaction manager. splits & merges
were affected by this, as they can update ids, as well as explicit id
changes (and fly type changes). but TM.generateTransactions looks to
see if there are transactions attached to the ACE, and this is now so
for splits & merges, and uses the attached trans rather than
converting (this is the new way im going with things). so the
conversion wasnt happening - and nor should it in genTrans. the
conversion should be data adapter specific - some data adapters - like
tair - may not want this conversion at all. 

so theres now a replaceIdUpdatesWithDelAndAdd method in TransMan that
is called by ChadoTransactionTransformer, so it is specific to chado
now. this needs to work on flat transactions. the transaction manager
can now track transactions in flattened & unflattened (with compound
trans) form. 

i fiddled with the idea of making a chado subclass of
TransactionOutputAdapter, but then realized the chado transaction
transformer was just as good a place for it - that this id change is
really part of the chado transform process. 

changed TransactionOutputAdapter.commit(List) to
commitTransactions(TransactionManager) shich allows the transformer to
call methods - like coalesce & repIdUpdates - on the
TransactionManager. 

CompoundTransaction now has a recursive getLeafTransactions
convenience method. 

corrected some bugs that were hard to find (nasty) due to trans man doing both
flattened & unflattened - the flattened trans has to be nulled out on
clear. 



Index: GAMEAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gamexml/GAMEAdapter.java,v
retrieving revision 1.137
retrieving revision 1.138
diff -C2 -d -r1.137 -r1.138
*** GAMEAdapter.java	20 May 2005 21:19:18 -0000	1.137
--- GAMEAdapter.java	31 May 2005 17:53:41 -0000	1.138
***************
*** 345,349 ****
          output.setTransformer(new ChadoTransactionTransformer());
          output.setTarget(fileName);
!         output.commit(curation.getTransactionManager().getTransactions());
        }
      }
--- 345,349 ----
          output.setTransformer(new ChadoTransactionTransformer());
          output.setTarget(fileName);
!         output.commitTransactions(curation.getTransactionManager());
        }
      }