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I tried to force this by changing the line "grep { $_ && (length($_) > 4000);" to "grep { $_ && (length($_) > 4000 || $_ > 4000);" but that was even worse: seq field in biosequence was null. Anyhow, the sequence should not have been updated after all, cos it was not changed. Any clues ? Thanks, Marc From Marc.Logghe at devgen.com Tue Feb 17 11:23:50 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Tue Feb 17 13:51:50 2004 Subject: [BioSQL-l] Query Problem. Message-ID: Hi, I was not able to figure it out completely, but found a fix. In Bio::DB::BioSQL::BiosequenceAdaptor the marked (#ml) line was added: sub get_persistent_slot_values { my ($self,$obj,$fkobjs) = @_; my @vals; if($obj->isa("Bio::Seq::RichSeqI")) { @vals = ($obj->seq_version()); } else { @vals = (undef); } #ml $obj->seq_has_changed(1) if $obj->length > 4000; push(@vals, $obj->length(), $obj->alphabet(), $obj->seq_has_changed() ? $obj->seq() : undef); return \@vals; } This forces an 'update' of the sequence if it is larger than 4000 bp. > -----Original Message----- > From: Marc Logghe > Sent: dinsdag 17 februari 2004 11:01 > To: biosql-l@open-bio.org > Subject: RE: [BioSQL-l] Query Problem. > > > Hi, > I have been trying to track down a nasty bug, but failed :-( > Sorry, Hilmar. > A biosequence containing more than 4000 nt is fine. No > problem in loading that. > A colleague of mine (FredericP) found out that as soon as you > add a feature to the corresponding bioentry later, and you do > an update (store+commit) your biosequence ends up truncated (4000). > Hoped that > Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver::get_sth > had to do something with it. > It appears that a different sth is chosen depending on e.g. > the field size (_upd_sth2 if length > 4000). I tried to force > this by changing the line "grep { $_ && (length($_) > 4000);" > to "grep { $_ && (length($_) > 4000 || $_ > 4000);" but that > was even worse: seq field in biosequence was null. > Anyhow, the sequence should not have been updated after all, > cos it was not changed. > Any clues ? > Thanks, > Marc > From hlapp at gnf.org Tue Feb 17 18:09:14 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Feb 17 18:15:32 2004 Subject: [BioSQL-l] Query Problem. In-Reply-To: Message-ID: <4D9974E7-619E-11D8-A489-000A959EB4C4@gnf.org> Hm, interesting. Basically, the trouble maker is that you cannot apply NVL() to LOB values. Biosequence.seq is of type CLOB. Normally, for every updated column the new value is wrapped in a call to NVL() to prevent overriding of values by incomplete objects (which would have certain attributes undefined instead of the value that's in the database). So, in order to protect column foo, you write the update statement as UPDATE blah SET ..., foo = NVL(?, foo), ... WHERE oid = ? If you bind undef to column foo's parameter, you get a no-change result without ever having to cross-check every attribute. This will work for the sequence so long as it is less than or equal to 4000 chars long, as then it will simply be treated as a VARCHAR2 and Oracle will cast it internally to CLOB when it gets assigned to the seq column. If the sequence length is longer than 4000 chars, you can't use NVL() on it, so there is special case code for Oracle that will edit the generated sql and replace the NVL() call with a direct assignment iff any of the object's attribute is defined and longer than 4000 chars in length. The get_persistent_slot_values() will return the sequence as having value undef if it hasn't changed in order to prevent unnecessary retrieval and update of a column of 10s/100s/1000s of kb if it hasn't changed. An unchanged sequence should therefore not lead to the NVL() clause to be edited away, because its value would be pretended as undef to the database update function. The unknown in this equation is what happens if in the NVL(?, foo) call the bound parameter is undef (NULL), but foo has more than 4000 chars. It shouldn't actually matter up to 32k chars length, as that is Oracle's upper limit for VARCHAR2 in PL/SQL (i.e., while DBI/DBD doesn't have its fingers in the game), and the NVL call is executed on the server, not the DBI client. Are you sure your threshold of misbehavior is 4000 and not 32k in length? If you turn on verbosity (call $db->verbose(1) after creating it), what parameters do you see get bound for the sequence that gets its sequence set to NULL after an update? -hilmar On Tuesday, February 17, 2004, at 08:23 AM, Marc Logghe wrote: > Hi, > I was not able to figure it out completely, but found a fix. > In Bio::DB::BioSQL::BiosequenceAdaptor the marked (#ml) line was added: > > sub get_persistent_slot_values { > my ($self,$obj,$fkobjs) = @_; > my @vals; > if($obj->isa("Bio::Seq::RichSeqI")) { > @vals = ($obj->seq_version()); > } else { > @vals = (undef); > } > #ml > $obj->seq_has_changed(1) if $obj->length > 4000; > > push(@vals, > $obj->length(), > $obj->alphabet(), > $obj->seq_has_changed() ? $obj->seq() : undef); > return \@vals; > } > > This forces an 'update' of the sequence if it is larger than 4000 bp. > >> -----Original Message----- >> From: Marc Logghe >> Sent: dinsdag 17 februari 2004 11:01 >> To: biosql-l@open-bio.org >> Subject: RE: [BioSQL-l] Query Problem. >> >> >> Hi, >> I have been trying to track down a nasty bug, but failed :-( >> Sorry, Hilmar. >> A biosequence containing more than 4000 nt is fine. No >> problem in loading that. >> A colleague of mine (FredericP) found out that as soon as you >> add a feature to the corresponding bioentry later, and you do >> an update (store+commit) your biosequence ends up truncated (4000). >> Hoped that >> Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver::get_sth >> had to do something with it. >> It appears that a different sth is chosen depending on e.g. >> the field size (_upd_sth2 if length > 4000). I tried to force >> this by changing the line "grep { $_ && (length($_) > 4000);" >> to "grep { $_ && (length($_) > 4000 || $_ > 4000);" but that >> was even worse: seq field in biosequence was null. >> Anyhow, the sequence should not have been updated after all, >> cos it was not changed. >> Any clues ? >> Thanks, >> Marc >> > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From gisel1 at msn.com Tue Feb 17 11:58:19 2004 From: gisel1 at msn.com (sean) Date: Tue Feb 17 19:02:37 2004 Subject: [BioSQL-l] Next Generation V-I-A-G-R-A! Not herbal! 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