For your entertainment
OK, I'm working on a project which involves developing microarray
designs. Currently there is a microarray module through which you can
create and array design object, add oligos (short DNA sequences) to it,
view it, output a galfile or csv file (just consider them types of
specialized reports), etc.
I've also written a simple interactive shell for manipulating these
designs. Where you see 'DNAcore Array Design: ' below is the readline
prompt. Please keep in mind that this is basically prototype code. The
modules will be kept but the interface will be improved later - probably
using CGI or other GUI. As a teaser, here's the error. More explination
below:
DNAcore Array Design: load array 2
SV = RV(0x88acf80) at 0x888d38c
REFCNT = 1
FLAGS = (ROK)
RV = 0x888d368
(in cleanup) dbih_getcom handle DBI::db=HASH(0x888d368) is not a
DBI handle (has no magic) at /usr/lib/perl5/site_perl/5.6.1
/DNAcore/DB.pm line 229.
SV = RV(0x848fe88) at 0xbffff380
REFCNT = 1
FLAGS = (ROK,READONLY)
RV = 0x888d368
Array 2 loaded
DNAcore Array Design: add oligos
Please enter SQL statement for getting oligos. Returned fields must be
oligo ID, oligo Name and Source Plate in that order. Extra fields may be
present, but will appear in galfile in the same order:
SELECT Origin_Key,ExternalReference_ID,Plate,CONCAT(Row,Col) FROM
DNAcore.Oligo,DNAcore.Well WHERE Oligo.ID = SourceID AND Source =
'Oligo' AND Plate = 40 ORDER BY Plate,Row,Col
DNAcore Array Design: create galfile
What I'm trying to add now is a way to save this object (hash) to a
database. Currently I'm just using Data::Dumper to serialize. The idea
is that a user can save a partially populated design (the structure has
room for more oligos) and work on it later. Or create new 'reports' at
any time [I'll probably keep this interface for myself regardless as a
simple way to test new methods ongoing]. The part that saves a design
works. When loading an existing design, the idea is to replace the array
object in use with the saved one - revivified from the database.
One other thing to note is that I have a DB module which wraps around
DBI. It has a bunch of methods covering many common needs and passes any
unrecognized calls directly to DBI (via AUTOLOAD). The array object
contains a connection to the database (a DB object returned by our
module), the reference to which is deleted before the object is dumped
and stored in the database. When the interface calls new to replace the
current object with the one the user wants to load, a fresh database
connection is made, the stored object is retrieved, the database
connection is added to the restored hash (same as if the object hash
defined without loading from the database), and the hash is blessed and
returned.
The error output you see below occurs during this recreation process.
Line 229 in DB.pm is the autoload passed call to DBI. At first I didn't
think I made any calls to the DBI after fetching the stored object.
After scratching my head a bit I noticed this line:
$self->{DBH} = $temp-{DBH};
Which, with some advanced debugging (read prints) has been verified as
the culprit. $self is the hashref created when the stored dump was
evale'd, which gets returned to new, blessed and returned to the user.
The actions taken afterthe error generated above, add oligos and create
galfile, both worked. The database added to the restored object works
fine.
Sean
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