[Biophp-dev] My humunguous posting - finally got it out of my system!

Nico Stuurman biophp-dev@bioinformatics.org
Mon, 9 Jun 2003 17:33:30 -0700

> Yesterday, Greg suggested using the BioSQL database schema for the Seq  
> object-to-SQL Database interface Nico and I were discussing.
> Initial reaction: Whoa, it's simply overwhelming!  But if Greg or  
> anyone here would volunteer to relate the pertinent table/columns to  
> what I have at http://genephp.sf.net/mysql_dbscripts.html, it would  
> certainly be a big help.
> Nonetheless, I proceeded to write some PHP code that generates SQL  
> INSERTs from data displayed on web forms.  You can find them at:
>    http://genephp.sf.net/parse_na_gb_par.html   [1]
>    http://genephp.sf.net/parse_na_gb_res.php    [2]
>    http://genephp.sf.net/insert_na_gb_res.php   [3]

Do these scripts work with the BioSQL database or with the tables you  
wrote?  I suggest to stick to the BioSQL layout and write the scripts  
necessary to insert a (biophp) seq object into this structure and to  
read them back out again.  No need to reinvent the wheel.

> Nico has graciously offered to help out in the MySQL-to-ADODB  
> conversion (so the SQL scripts could be used for other RDBMs).
> If anyone would like to work on a MySQL-to-PearDB conversion of the  
> CREATEs in  http://genephp.sf.net/mysql_dbscripts.html,
> or the INSERTs at insert_na_gb_res.php, you're mighty welcome!

PEAR and adodb basically do the same thing.  Since you really do not  
need to 'install' anything to get either PEAR or adodb to work (you  
simply have to download one or the other) and I don't think we are  
ready to spread our resources by using both of them, it makes sense to  
choose one or the other.  Sean's argument for using PEAR is that is  
standard (since it is distributed with php).  My two arguments for  
adodb are: 1.  I have experience working with making it a lot of easier  
to develop quickly with adodb, and 2. it appears to be twice as fast as  
PEAR (at least according to php.weblog.com.  Maybe the choice should  
come down to the people who are going to write the code...

> If anyone would also like to work on a DATABASE SCHEMA for data  
> extracted by the various parser scripts (there are 30 formats  
> supported fully/partially at http://genephp.sf.net/io_set.html), well,  
> that would be swell...

All great and nice, but I don't see any of the code...  What are you  
parsing into?  Are you using the seqIOimport  
seqIOimport.inc.php) class are something completely different?   
Sometimes I have the feeling we are not really working together here...