[BioSQL-l] Pg and mysql versions are decoupled

[Hilmar Lapp]

First, I got frustrated yesterday about the transfrom.pl script unable 
to parse the latest mysql schema version, although it's really not too 
special. What's really frustrating is that the RecDescent parse 
apparently yields a truncated document tree in a silent fashion, and 
I'm not going to debug Parse::RecDescent. I suspect the problem is that 
the token DEFAULT interferes with an internal interpretation of a 
DEFAULT rule.

Second, I added the rules suggested by Yves Bastide to the Pg version 
of the schema. As soon as we agree on marching towards schema freeze, 
I'll then update the Pg mapping drivers of bioperl-db, and I honestly 
hope that then Pg can become a first-class supported RDBMS for biosql. 
It's just so much more powerful than MySQL. I tested the effect of the 
rules in DBI statement return values. If the rules fire then the return 
value is 0E0 instead of 1, which as a string also evaluates to TRUE in 
perl, but can be tested against 0 (which will test true, unlike - 
obviously - the value '1'). So, a 'failed' insert (that is, an insert 
that would have failed if it had been permitted) can be easily and 
relatively cleanly detected in code. This removes a serious obstacle 
for using biosql under Pg in a way that causes minimal impact on the 
existing codebase, and can be easily taken advantage of in other Bio* 
projects too. Thanks for this tip Yves.

I'm ending this email with the proposal to abandon the transform_sql.pl 
script, unless someone is serious about debugging and fixing it. If we 
were to continue using it, the CREATE RULE section from biosqldb-pg.sql 
would have to be moved into a separate file. Any takers? Any votes?

	-hilmar
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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