[BioSQL-l] latest versions for bioperl-db biosql-schema ?

[Hilmar Lapp]

On Thursday, April 17, 2003, at 07:50  AM, Kris Boulez wrote:

>
> As promised, here are some more warnings/errors from running make test.
> A best effort for locating the problem is given.
>
>
> dblink.t (and ensembl.t, fuzzy2.t genbank.t)
> --------
> a message is printed like
>
>   DBD::mysql::st bind_param failed: Illegal parameter number at
>   blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1081, <GEN0>
>   line 72.
>
> This seems to come from the following evaled code
>
>       eval { $rv = $sth->bind_param($i, $qvalues->[$i-1]); };
>
> (return value is checked, but DBD::mysql is chatty)
>

That's OK. The whole code still being pretty young, I prefer to see all 
those messages. I can, however, see that it confuses or annoys people. 
You can silence the DBD driver by adding PrintError => 0 in line 71 in 
Bio/DB/BioSQL/DBAdaptor.pm.

>
> ePCRdb.t
> --------
> The third test (of three) fails with
>
>   Can't locate object method "get_MapAdaptor" via package
>   "Bio::DB::BioSQL::DBAdaptor" at t/ePCRdb.t line 29.
>

You should also see map.t and marker.t failing with the same message. 
The reason is a misconfiguration in t/DBHarness.markerdb.conf: the key 
database needs to have the value 'map' in this file:

     # The name of the database within bioperl-db (biosql or map)
     'database'      => 'map',

> The code in question is
>
>   my $mapadaptor = $db->get_MapAdaptor();
>
> get_Mapadaptor() is defined in Bio/DB/Map/DBAdaptor.pm
>
>
>
>
> locuslink.t
> -----------
> An exception is thrown after test 4
>
>   ------------- EXCEPTION Bio::Root::NotImplemented -------------
>   MSG: Abstract method "Bio::Ontology::TermI::get_dblinks" is not
>   implemented by package Bio::Annotation::OntologyTerm.
>   This is not your fault - author of Bio::Annotation::OntologyTerm
>   should be blamed!
>
> Perhaps I need the latest code from bioperl-live cvs ?
>
>

Yes. Or the latest code from bioperl tag branch-1-2. Or you apply the 
enclosed patch with

	$ patch -p0 < onto-term.patch

to your bioperl source tree (bioperl-live or 1.2.1), then re-install. 
This one I discovered only after 1.2.1 had been released, but the patch 
is really simple.

>
> remove.t
> --------
> Gives multiple warnings (again from DBD::mysql) like
>
>   DBD::mysql::st execute failed: Duplicate entry '1-1-1' for key 1 at
>   blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, <GEN0> 
> line
>   282.
>   DBD::mysql::st execute failed: Duplicate entry '1-2-2' for key 1 at
>   blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, <GEN0> 
> line
>   282.
>   DBD::mysql::st execute failed: Duplicate entry '1-3-3' for key 1 at
>   blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, <GEN0> 
> line
>   282.
>
> This is for the code starting around line 90 of remove.t ("test
> removing associations").
>

Again, these warnings are alright. If you want to shut it up then add 
PrintError => 0 as I mentioned above. Generally speaking, DBD failure 
messages alone shouldn't be reason for concern, as the return values 
are (almost?) always checked. What's potentially more concerning is if 
you start seeing warning messages in the familiar bioperl formatting:

-----------------
MSG: warning text here
-----------------

And exception stack traces of course ...

Let me know if you encounter more problems.

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

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