From d49228002 at ym.edu.tw  Thu Jun  1 09:32:00 2006
From: d49228002 at ym.edu.tw (Yi-Feng Chang)
Date: Thu, 01 Jun 2006 21:32:00 +0800
Subject: [BioSQL-l] Error loading ontology terms
Message-ID: <447EEC50.9090807@ym.edu.tw>

Dear All,
I've checked biosql archives, and found a similar thread
(http://lists.open-bio.org/pipermail/biojava-l/2005-November/005151.html)
however, it did not give specific solution. So I post here again, and
hope there are someone could help me.
I'm using JDK1.5.0_05, Biojava 1.4, Biosql 1.41, and Mysql 5.0 with
My_connectJ 3.1
I was following the demo source that provide by biojava-in-anger except
for the database connection
the exceptions were listed in following:
In first connection there would be a connection error
*** Importing a core ontology -- hope this is okay
*** Importing terms
Exception in thread "main" org.biojava.bio.BioException: Error
connecting to BioSQL database: Connection is closed.
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:276)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:194)
at genevote.BioSQLTest.loadSeq(BioSQLTest.java:31)
at genevote.BioSQLTest.main(BioSQLTest.java:70)
Caused by: java.sql.SQLException: Connection is closed.
at
org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.checkOpen(PoolingDataSource.java:219)
at
org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.createStatement(PoolingDataSource.java:248)
at
org.biojava.bio.seq.db.biosql.MySQLDBHelper.getInsertID(MySQLDBHelper.java:68)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:268)
... 3 more
Then I tried again, it works, and I put all sequences in genbank format
into biosql db without error.
But, while I tried to extract sequences, exception comes again.
org.biojava.bio.BioException: Error loading ontology terms
at
org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology(OntologySQL.java:444)
at
org.biojava.bio.seq.db.biosql.OntologySQL.getOntology(OntologySQL.java:116)
at org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java:413)
at
org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL(OntologySQL.java:72)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:240)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:194)
at genevote.test.loadSeq(test.java:25)
at genevote.test.main(test.java:76)
Caused by: java.sql.SQLException: Unknown column 'name' in 'field list'
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2851)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1534)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1625)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2297)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2226)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1812)
at
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1657)
at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:205)
at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:205)
at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms(OntologySQL.java:339)
at
org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology(OntologySQL.java:441)
... 7 more

yi-feng chang



From d49228002 at ym.edu.tw  Fri Jun  2 02:31:45 2006
From: d49228002 at ym.edu.tw (Yi-Feng Chang)
Date: Fri, 02 Jun 2006 14:31:45 +0800
Subject: [BioSQL-l] [Biojava-l] Error loading ontology terms
In-Reply-To: <447FD342.4090806@uni-tuebingen.de>
References: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
	<1149175573.3948.78.camel@texas.ebi.ac.uk>
	<447FD342.4090806@uni-tuebingen.de>
Message-ID: <447FDB51.9090500@ym.edu.tw>

Thanks, your solution is right.
I solve this problem.
Many thanks.

ian

Andreas Dr?ger wrote:
> Hello,
>
> You can solve this problem just by renaming the column "synonym" in
> table "term_synonym" to "name". The reason for changing the name of
> this column is that in some database systems the term "synonym" is a
> reserved word. So the older version that you are using currently might
> cause problems with some databas systems. Once you renamed this
> column, BioJava will work fine.
>
> Andreas Dr?ger
>
>> java.sql.SQLException: Unknown column 'name' in 'field list'
>>
>>
>



From andreas.draeger at uni-tuebingen.de  Fri Jun  2 01:57:22 2006
From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=)
Date: Fri, 02 Jun 2006 07:57:22 +0200
Subject: [BioSQL-l] [Biojava-l] Error loading ontology terms
In-Reply-To: <1149175573.3948.78.camel@texas.ebi.ac.uk>
References: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
	<1149175573.3948.78.camel@texas.ebi.ac.uk>
Message-ID: <447FD342.4090806@uni-tuebingen.de>

Hello,

You can solve this problem just by renaming the column "synonym" in 
table "term_synonym" to "name". The reason for changing the name of this 
column is that in some database systems the term "synonym" is a reserved 
word. So the older version that you are using currently might cause 
problems with some databas systems. Once you renamed this column, 
BioJava will work fine.

Andreas Dr?ger

>	java.sql.SQLException: Unknown column 'name' in 'field list'
>  
>

-- 
Dipl.-Bioinform. Andreas Dr?ger
Eberhard Karls University T?bingen
Center for Bioinformatics (ZBIT)
Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091


From richard.holland at ebi.ac.uk  Thu Jun  1 11:26:12 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Thu, 01 Jun 2006 16:26:12 +0100
Subject: [BioSQL-l] Error loading ontology terms
In-Reply-To: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
References: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
Message-ID: <1149175573.3948.78.camel@texas.ebi.ac.uk>

Hi there.

I looked through your stack trace, and the line numbers don't match up
with the current code. I have a strong feeling you may have an out-of-
date version of biojava.

Could you double-check that you have the latest biojava-1.4 version, or
are using the biojava-live version built from CVS?

If you can confirm that you are using the latest 1.4 or biojava-live
then it'd be easier to solve this.

Alternatively, you could have an out-of-date version of the BioSQL
schema. 

The reason I suspect that your BioSQL or BioJava are out of date is
because in the last stack trace you mention, this exception arises:

	java.sql.SQLException: Unknown column 'name' in 'field list'

This shows that BioJava has expected to find a column called 'name' in
some table in BioSQL, but that column is not there. This would only
happen if your BioSQL version did not match the version of BioSQL that
your version of BioJava was expecting.

cheers,
Richard

On Thu, 2006-06-01 at 21:32 +0800, Yi-Feng Chang wrote:
> Leif, this looks more like a biojava or biojava-x related problem, so  
> I'm resending it to the Biojava list. -hilmar
> ======================================================================== 
> ==
> Dear All,
> I've checked biosql archives, and found a similar thread
> (http://lists.open-bio.org/pipermail/biojava-l/2005-November/ 
> 005151.html)
> however, it did not give specific solution. So I post here again, and
> hope there are someone could help me.
> I'm using JDK1.5.0_05, Biojava 1.4, Biosql 1.41, and Mysql 5.0 with
> My_connectJ 3.1
> I was following the demo source that provide by biojava-in-anger except
> for the database connection
> the exceptions were listed in following:
> In first connection there would be a connection error
> *** Importing a core ontology -- hope this is okay
> *** Importing terms
> Exception in thread "main" org.biojava.bio.BioException: Error
> connecting to BioSQL database: Connection is closed.
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:276)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
> at genevote.BioSQLTest.loadSeq(BioSQLTest.java:31)
> at genevote.BioSQLTest.main(BioSQLTest.java:70)
> Caused by: java.sql.SQLException: Connection is closed.
> at
> org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.checkOpen(PoolingDataSource.java:219)
> at
> org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.createStatement(PoolingDataSource.java:248)
> at
> org.biojava.bio.seq.db.biosql.MySQLDBHelper.getInsertID 
> (MySQLDBHelper.java:68)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:268)
> ... 3 more
> Then I tried again, it works, and I put all sequences in genbank format
> into biosql db without error.
> But, while I tried to extract sequences, exception comes again.
> org.biojava.bio.BioException: Error loading ontology terms
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:444)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.getOntology 
> (OntologySQL.java:116)
> at org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java: 
> 413)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL 
> (OntologySQL.java:72)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:240)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
> at genevote.test.loadSeq(test.java:25)
> at genevote.test.main(test.java:76)
> Caused by: java.sql.SQLException: Unknown column 'name' in 'field list'
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2851)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1534)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1625)
> at com.mysql.jdbc.Connection.execSQL(Connection.java:2297)
> at com.mysql.jdbc.Connection.execSQL(Connection.java:2226)
> at
> com.mysql.jdbc.PreparedStatement.executeInternal 
> (PreparedStatement.java:1812)
> at
> com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java: 
> 1657)
> at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
> at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
> at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms 
> (OntologySQL.java:339)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:441)
> ... 7 more
> 
> yi-feng chang
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416


From n.saunders at uq.edu.au  Tue Jun  6 01:41:34 2006
From: n.saunders at uq.edu.au (Neil Saunders)
Date: Tue, 06 Jun 2006 15:41:34 +1000
Subject: [BioSQL-l] Problem loading GenPept files into mysql biosql
Message-ID: <4485158E.2010202@uq.edu.au>

hi,

I've installed the MySQL BioSQL schema (Ubuntu Linux 5.10, BioPerl 1.5, MySQL 
4.1.12).  I have written a script that uses Bio::DB::GenPept to retrieve files 
by GI and then tries to load them using load_seqdatabase.pl:

load_seqdatabase.pl --safe --dbname DBNAME --dbuser DBUSER --dbpass DBPASS 
--namespace genpept --format genbank <files>

I'm getting a lot of errors of type:

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were 
("","Direct Submission","Submitted (11-SEP-2004) National Center for 
Biotechnology Information, NIH, Bethesda, MD 20894, 
USA","CRC-EFE0D20CE0E07E7D","1","637","") FKs (<NULL>)
Duplicate entry 'CRC-EFE0D20CE0E07E7D' for key 3
---------------------------------------------------

This seems to be related to a similar problem using UniProt discussed on this list:

http://lists.open-bio.org/pipermail/biosql-l/2006-May/000977.html

Am I right in thinking that a CRC is generated from the JOURNAL line of a 
GenPept file and that non-unique CRCs are causing this problem?  My GenPept 
files are actually RefSeq entries from complete microbial genomes.  An example 
would be NP_378145 (GI 15922476).  The REFERENCE for such records is often 
"Direct Submission" rather than a journal and obviously in these cases, the set 
of all proteins from a genome has the same REFERENCE, so unique CRCs don't seem 
like a good idea.

I'd be grateful if anyone could confirm that these records are a problem and 
suggest any workarounds,

thanks,
Neil
-- 
  School of Molecular and Microbial Sciences
  University of Queensland
  Brisbane 4072 Australia

http://psychro.bioinformatics.unsw.edu.au/neil

From cjfields at uiuc.edu  Tue Jun  6 10:49:15 2006
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 6 Jun 2006 09:49:15 -0500
Subject: [BioSQL-l] Problem loading GenPept files into mysql biosql
In-Reply-To: <4485158E.2010202@uq.edu.au>
Message-ID: <000b01c68978$620a2270$15327e82@pyrimidine>

I had similar issues with these files.  Hilmar had this to say in a previous
post to bioperl-l:

http://article.gmane.org/gmane.comp.lang.perl.bio.general/10068

> I would generally advise against taking Uniprot/Swissprot entries from
> their GenPept reincarnation. The formats are incompatible in some
> aspects (e.g., Swissprot, like EMBL, has first-level db_xrefs, whereas
> GenBank format doesn't; instead it puts db_xrefs into the feature
> table).

If you really need these sequences, you should probably grab them from
UniProt/SwissProt directly and use 'swiss' Bio::SeqIO format.  I never found
a use for them since there was normally a properly-parsed GenBank
counterpart (though I hate the fact that they seemingly clog up the works).
We probably should have some warning added for these sequences in bioperl or
bioperl-db if this keeps popping up, though.

Chris

> -----Original Message-----
> From: biosql-l-bounces at lists.open-bio.org [mailto:biosql-l-
> bounces at lists.open-bio.org] On Behalf Of Neil Saunders
> Sent: Tuesday, June 06, 2006 12:42 AM
> To: biosql-l at lists.open-bio.org
> Subject: [BioSQL-l] Problem loading GenPept files into mysql biosql
> 
> hi,
> 
> I've installed the MySQL BioSQL schema (Ubuntu Linux 5.10, BioPerl 1.5,
> MySQL
> 4.1.12).  I have written a script that uses Bio::DB::GenPept to retrieve
> files
> by GI and then tries to load them using load_seqdatabase.pl:
> 
> load_seqdatabase.pl --safe --dbname DBNAME --dbuser DBUSER --dbpass DBPASS
> --namespace genpept --format genbank <files>
> 
> I'm getting a lot of errors of type:
> 
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values
> were
> ("","Direct Submission","Submitted (11-SEP-2004) National Center for
> Biotechnology Information, NIH, Bethesda, MD 20894,
> USA","CRC-EFE0D20CE0E07E7D","1","637","") FKs (<NULL>)
> Duplicate entry 'CRC-EFE0D20CE0E07E7D' for key 3
> ---------------------------------------------------
> 
> This seems to be related to a similar problem using UniProt discussed on
> this list:
> 
> http://lists.open-bio.org/pipermail/biosql-l/2006-May/000977.html
> 
> Am I right in thinking that a CRC is generated from the JOURNAL line of a
> GenPept file and that non-unique CRCs are causing this problem?  My
> GenPept
> files are actually RefSeq entries from complete microbial genomes.  An
> example
> would be NP_378145 (GI 15922476).  The REFERENCE for such records is often
> "Direct Submission" rather than a journal and obviously in these cases,
> the set
> of all proteins from a genome has the same REFERENCE, so unique CRCs don't
> seem
> like a good idea.
> 
> I'd be grateful if anyone could confirm that these records are a problem
> and
> suggest any workarounds,
> 
> thanks,
> Neil
> --
>   School of Molecular and Microbial Sciences
>   University of Queensland
>   Brisbane 4072 Australia
> 
> http://psychro.bioinformatics.unsw.edu.au/neil
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l


From hlapp at gmx.net  Wed Jun  7 08:52:22 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 7 Jun 2006 08:52:22 -0400
Subject: [BioSQL-l] [Bioperl-l] bioperl-db failing tests
In-Reply-To: <2000234931344D4BA434A0C235D1956B0C4852@hsv-exmail02.operonads.local>
References: <2000234931344D4BA434A0C235D1956B0C4852@hsv-exmail02.operonads.local>
Message-ID: <4F23D2EA-2218-4023-A3F6-3284912952BE@gmx.net>

Hi Michael,

Bioperl-db will open all connections with AutoCommit => 0 in the DBI  
parameter hash. The test you're stumbling over is actually there to  
test that the database  does support transactions, but apparently in  
5.x versions MySQL no longer silently ignores the AutoCommit  
parameter if it doesn't support transactions (effectively preempting  
the test ...).

Now you say that innodb shows as enabled - i.e., you can confirm that  
you changed the Mysql configuration parameter that designates the  
directory for innodb to store its files?

You can confirm that transactions are supported by simple tests on  
the sql level. Open a mysql shell and do the following:

	-- BTW 'start transaction;' will (should) work too
	mysql> set autocommit = 0;
	mysql> insert into biodatabase (name) values ('__dummy__');
	mysql> select name from biodatabase where name = '__dummy__';
	mysql> rollback;
	mysql> select name from biodatabase where name = '__dummy__';

The first SELECT query should return one and the last query should  
return zero rows if transactions are supported, and there shouldn't  
be any error.

If the above succeeds (which I don't expect it to) then it looks like  
the DBD::mysql driver thinks the database doesn't support  
transactions when in reality it does. Let me know the result.

	-hilmar

On Jun 6, 2006, at 2:34 PM, Michael Muratet US-Huntsville wrote:

> Greetings
>
> I am trying to install bioperl-db in preparation for installing a  
> biosql database. I'm running on a Dell PowerEdge with quad dual- 
> core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl  
> 1.5.1.  I have installed mysql v5.0.21 from source with --with- 
> innodb set for the configuration. I installed bioperl-db from cvs.  
> I have the latest DBI and DBD:mysql installed a few weeks ago from  
> CPAN. The installation has been working well with perl otherwise,  
> for example, the Ensembl core API works OK. SHOW ENGINES indicates  
> that innodb is enabled.  I have attached a snippet from the top of  
> the output below. I searched the web and the bioperl-db list and  
> haven't found anything that appears to be relevant. I've done  
> several of these installs and they've pretty much completed without  
> a single glitch. Does anyone have any ideas how to isolate the  
> problem?
>
> Thanks
>
> Mike
>
> [mmuratet at HSV-PROBE bioperl-db]$ make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"  
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/01dbadaptor.....ok 14/19
> ------------- EXCEPTION  -------------
> MSG: failed to open connection: Transactions not supported by database
> STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:255
> STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:215
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/ 
> site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/ 
> BioSQL/BasePersistenceAdaptor.pm:1477
> STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/ 
> perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/ 
> DB/BioSQL/BaseDriver.pm:518
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
> STACK toplevel t/01dbadaptor.t:62
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From Michael.Muratet at operon.com  Tue Jun  6 14:34:38 2006
From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville)
Date: Tue, 6 Jun 2006 13:34:38 -0500
Subject: [BioSQL-l] bioperl-db failing tests
Message-ID: <2000234931344D4BA434A0C235D1956B0C4852@hsv-exmail02.operonads.local>

Greetings

I am trying to install bioperl-db in preparation for installing a biosql database. I'm running on a Dell PowerEdge with quad dual-core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl 1.5.1.  I have installed mysql v5.0.21 from source with --with-innodb set for the configuration. I installed bioperl-db from cvs. I have the latest DBI and DBD:mysql installed a few weeks ago from CPAN. The installation has been working well with perl otherwise, for example, the Ensembl core API works OK. SHOW ENGINES indicates that innodb is enabled.  I have attached a snippet from the top of the output below. I searched the web and the bioperl-db list and haven't found anything that appears to be relevant. I've done several of these installs and they've pretty much completed without a single glitch. Does anyone have any ideas how to isolate the problem?

Thanks

Mike

[mmuratet at HSV-PROBE bioperl-db]$ make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01dbadaptor.....ok 14/19
------------- EXCEPTION  -------------
MSG: failed to open connection: Transactions not supported by database
STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:255
STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:215
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1477
STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BaseDriver.pm:518
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
STACK toplevel t/01dbadaptor.t:62



From david at autohandle.com  Wed Jun  7 11:45:41 2006
From: david at autohandle.com (David Scott)
Date: Wed, 07 Jun 2006 08:45:41 -0700
Subject: [BioSQL-l] value field in seqfeature_qualifier_value too small
Message-ID: <4486F4A5.3010602@autohandle.com>

in seqfeature_qualifier_value:
 
  SEQFEATURE_ID                             NOT NULL NUMBER(38)
  TERM_ID                                   NOT NULL NUMBER(38)
  RANK                                      NOT NULL NUMBER(3)
  VALUE                                              VARCHAR2(4000)
 
 the value field is restricted to 4000 bytes - 4000 bytes too small to 
 carry current genbank protein translations - e.g. AB016240.1 has a 
 protein translation of 4133 characters. since 4000 bytes is a string 
 length restriction for some jdbc drivers - to increase the field size, 
 the field type should also be changed to clob.


From hlapp at gmx.net  Wed Jun  7 13:15:49 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 7 Jun 2006 13:15:49 -0400
Subject: [BioSQL-l] value field in seqfeature_qualifier_value too small
In-Reply-To: <4486F4A5.3010602@autohandle.com>
References: <4486F4A5.3010602@autohandle.com>
Message-ID: <39531248-B1A0-4911-9F4A-6D97D050B0A3@gmx.net>

You may make this change in your installation, and I should maybe  
document this possibility in the schema.

However, there are some serious issues with doing so. First off, you  
will no longer be able to search by simple query (you'd have to use  
DBMS_LOB functions), and you can't index the column any more.  
Furthermore, all language bindings will need special code to use the  
stream or other LOB API for getting/setting the value. There's  
additional issues that LOB columns raise compared to VARCHAR types.

It's worth noting that this applies so far only to Oracle (the other  
RDBMSs do not impose the length restriction), and it's in reality  
only the value of the protein translation feature tag that exceeds  
the limit on occasion.

I personally strip the protein translation tag from all loaded  
Genbank and RefSeq records because the value may be computed easily  
on the fly, and the respective sequences are usually there too unless  
you don't load Genpept or the NP_/XP_* part of RefSeq - but in this  
case I don't understand why you would want the tag value but not the  
full sequence.

Not the easy answer you may have hoped for, and I'd welcome any  
suggestions for how the problem could be solved w/o using CLOBs.

	-hilmar

On Jun 7, 2006, at 11:45 AM, David Scott wrote:

> in seqfeature_qualifier_value:
>
>   SEQFEATURE_ID                             NOT NULL NUMBER(38)
>   TERM_ID                                   NOT NULL NUMBER(38)
>   RANK                                      NOT NULL NUMBER(3)
>   VALUE                                              VARCHAR2(4000)
>
>  the value field is restricted to 4000 bytes - 4000 bytes too small to
>  carry current genbank protein translations - e.g. AB016240.1 has a
>  protein translation of 4133 characters. since 4000 bytes is a string
>  length restriction for some jdbc drivers - to increase the field  
> size,
>  the field type should also be changed to clob.
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From hlapp at gmx.net  Wed Jun  7 13:25:25 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 7 Jun 2006 13:25:25 -0400
Subject: [BioSQL-l] [Bioperl-l] bioperl-db failing tests
In-Reply-To: <2000234931344D4BA434A0C235D1956B0C485C@hsv-exmail02.operonads.local>
References: <2000234931344D4BA434A0C235D1956B0C485C@hsv-exmail02.operonads.local>
Message-ID: <76434774-51A4-46E7-97AA-1E9227CB7771@gmx.net>

Hi Michael,

yes it looks like a problem in DBD if DBD::mysql fails to recognize  
that the mysql instance to which it is connected does support  
transactions. You can verify this by writing a simple script that  
tries to open a connection with
{ AutoCommit => 0 } as the parameter hash:

	use DBI;
	my $dbh = DBI->connect("dbi:mysql:database=<yourdb>;host=<yourhost>",
	                       "username","password",
	                       { AutoCommit => 0, RaiseError => 0 });
	die DBI::errstr unless $dbh;
	$dbh->disconnect;

If this succeeds fine then something in Biosql may be related to the  
problem, but otherwise not.

	-hilmar


On Jun 7, 2006, at 12:01 PM, Michael Muratet US-Huntsville wrote:

> Hilmar
>
> Pardon the top post.
>
> I tried the test below and it failed. So, I went back and redid the  
> Innodb configuration (deleted all the index files--they were empty  
> anyway, reinstalled biosql (which was empty,too) and restarted the  
> server. Now, the test below works. I went into the DBD-3.0003 and  
> did a distclean and reinstalled the package, but it fails the one  
> transaction test, too. So, it looks like the problem is in DBD, yes?
>
> We had a RAID 5 drive glitch the day before yesterday and rebuilt  
> it. That's the only thing that's changed that I know of that could  
> have caused the problem with ibxxx files.
>
> I have received a reply on the DBD list. Can you think of anything  
> else I should try from the biosql end?
>
> Thanks a million.
>
> Mike
>
> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Wednesday, June 07, 2006 7:52 AM
> To: Michael Muratet US-Huntsville
> Cc: Bioperl; BioSQL
> Subject: Re: [Bioperl-l] bioperl-db failing tests
>
>
> Hi Michael,
>
> Bioperl-db will open all connections with AutoCommit => 0 in the DBI
> parameter hash. The test you're stumbling over is actually there to
> test that the database  does support transactions, but apparently in
> 5.x versions MySQL no longer silently ignores the AutoCommit
> parameter if it doesn't support transactions (effectively preempting
> the test ...).
>
> Now you say that innodb shows as enabled - i.e., you can confirm that
> you changed the Mysql configuration parameter that designates the
> directory for innodb to store its files?
>
> You can confirm that transactions are supported by simple tests on
> the sql level. Open a mysql shell and do the following:
>
> 	-- BTW 'start transaction;' will (should) work too
> 	mysql> set autocommit = 0;
> 	mysql> insert into biodatabase (name) values ('__dummy__');
> 	mysql> select name from biodatabase where name = '__dummy__';
> 	mysql> rollback;
> 	mysql> select name from biodatabase where name = '__dummy__';
>
> The first SELECT query should return one and the last query should
> return zero rows if transactions are supported, and there shouldn't
> be any error.
>
> If the above succeeds (which I don't expect it to) then it looks like
> the DBD::mysql driver thinks the database doesn't support
> transactions when in reality it does. Let me know the result.
>
> 	-hilmar
>
> On Jun 6, 2006, at 2:34 PM, Michael Muratet US-Huntsville wrote:
>
>> Greetings
>>
>> I am trying to install bioperl-db in preparation for installing a
>> biosql database. I'm running on a Dell PowerEdge with quad dual-
>> core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl
>> 1.5.1.  I have installed mysql v5.0.21 from source with --with-
>> innodb set for the configuration. I installed bioperl-db from cvs.
>> I have the latest DBI and DBD:mysql installed a few weeks ago from
>> CPAN. The installation has been working well with perl otherwise,
>> for example, the Ensembl core API works OK. SHOW ENGINES indicates
>> that innodb is enabled.  I have attached a snippet from the top of
>> the output below. I searched the web and the bioperl-db list and
>> haven't found anything that appears to be relevant. I've done
>> several of these installs and they've pretty much completed without
>> a single glitch. Does anyone have any ideas how to isolate the
>> problem?
>>
>> Thanks
>>
>> Mike
>>
>> [mmuratet at HSV-PROBE bioperl-db]$ make test
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>> t/01dbadaptor.....ok 14/19
>> ------------- EXCEPTION  -------------
>> MSG: failed to open connection: Transactions not supported by  
>> database
>> STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/
>> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm: 
>> 255
>> STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/
>> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm: 
>> 215
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/
>> site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/
>> BioSQL/BasePersistenceAdaptor.pm:1477
>> STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/
>> perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/
>> DB/BioSQL/BaseDriver.pm:518
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /
>> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/
>> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /
>> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/
>> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
>> STACK toplevel t/01dbadaptor.t:62
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From Michael.Muratet at operon.com  Wed Jun  7 12:01:29 2006
From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville)
Date: Wed, 7 Jun 2006 11:01:29 -0500
Subject: [BioSQL-l] [Bioperl-l] bioperl-db failing tests
Message-ID: <2000234931344D4BA434A0C235D1956B0C485C@hsv-exmail02.operonads.local>

Hilmar

Pardon the top post.

I tried the test below and it failed. So, I went back and redid the Innodb configuration (deleted all the index files--they were empty anyway, reinstalled biosql (which was empty,too) and restarted the server. Now, the test below works. I went into the DBD-3.0003 and did a distclean and reinstalled the package, but it fails the one transaction test, too. So, it looks like the problem is in DBD, yes?

We had a RAID 5 drive glitch the day before yesterday and rebuilt it. That's the only thing that's changed that I know of that could have caused the problem with ibxxx files. 

I have received a reply on the DBD list. Can you think of anything else I should try from the biosql end?

Thanks a million.

Mike

-----Original Message-----
From: Hilmar Lapp [mailto:hlapp at gmx.net]
Sent: Wednesday, June 07, 2006 7:52 AM
To: Michael Muratet US-Huntsville
Cc: Bioperl; BioSQL
Subject: Re: [Bioperl-l] bioperl-db failing tests


Hi Michael,

Bioperl-db will open all connections with AutoCommit => 0 in the DBI  
parameter hash. The test you're stumbling over is actually there to  
test that the database  does support transactions, but apparently in  
5.x versions MySQL no longer silently ignores the AutoCommit  
parameter if it doesn't support transactions (effectively preempting  
the test ...).

Now you say that innodb shows as enabled - i.e., you can confirm that  
you changed the Mysql configuration parameter that designates the  
directory for innodb to store its files?

You can confirm that transactions are supported by simple tests on  
the sql level. Open a mysql shell and do the following:

	-- BTW 'start transaction;' will (should) work too
	mysql> set autocommit = 0;
	mysql> insert into biodatabase (name) values ('__dummy__');
	mysql> select name from biodatabase where name = '__dummy__';
	mysql> rollback;
	mysql> select name from biodatabase where name = '__dummy__';

The first SELECT query should return one and the last query should  
return zero rows if transactions are supported, and there shouldn't  
be any error.

If the above succeeds (which I don't expect it to) then it looks like  
the DBD::mysql driver thinks the database doesn't support  
transactions when in reality it does. Let me know the result.

	-hilmar

On Jun 6, 2006, at 2:34 PM, Michael Muratet US-Huntsville wrote:

> Greetings
>
> I am trying to install bioperl-db in preparation for installing a  
> biosql database. I'm running on a Dell PowerEdge with quad dual- 
> core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl  
> 1.5.1.  I have installed mysql v5.0.21 from source with --with- 
> innodb set for the configuration. I installed bioperl-db from cvs.  
> I have the latest DBI and DBD:mysql installed a few weeks ago from  
> CPAN. The installation has been working well with perl otherwise,  
> for example, the Ensembl core API works OK. SHOW ENGINES indicates  
> that innodb is enabled.  I have attached a snippet from the top of  
> the output below. I searched the web and the bioperl-db list and  
> haven't found anything that appears to be relevant. I've done  
> several of these installs and they've pretty much completed without  
> a single glitch. Does anyone have any ideas how to isolate the  
> problem?
>
> Thanks
>
> Mike
>
> [mmuratet at HSV-PROBE bioperl-db]$ make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"  
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/01dbadaptor.....ok 14/19
> ------------- EXCEPTION  -------------
> MSG: failed to open connection: Transactions not supported by database
> STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:255
> STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:215
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/ 
> site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/ 
> BioSQL/BasePersistenceAdaptor.pm:1477
> STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/ 
> perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/ 
> DB/BioSQL/BaseDriver.pm:518
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
> STACK toplevel t/01dbadaptor.t:62
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From hlapp at gmx.net  Sat Jun 10 23:45:01 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 10 Jun 2006 23:45:01 -0400
Subject: [BioSQL-l] Error loading ontology terms
In-Reply-To: <000001c68c97$f461ac70$6801a8c0@iannb>
References: <000001c68c97$f461ac70$6801a8c0@iannb>
Message-ID: <90FF3359-AA97-4F6D-9A7D-8AA8E0590A10@gmx.net>

The specific solution is in the biojava list archives, not the biosql  
list. If I remember correctly, you need to either upgrade biojava or  
biosql or both to the latest revision.

	-hilmar

On May 31, 2006, at 10:39 AM, Yi-Feng Chang wrote:

> Dear All,
> I've checked biosql archives, and found a similar thread (http:// 
> lists.open-bio.org/pipermail/biojava-l/2005-November/005151.html)  
> however, it did not give specific solution. So I post here again,  
> and hope there are someone could help me.
> I'm using JDK1.5.0_05, Biojava 1.4, Biosql 1.41, and Mysql 5.0 with  
> My_connectJ 3.1
>
> I was following the demo source that provide by biojava-in-anger  
> except for the database connection
> the exceptions were listed in following:
>
> In first connection there would be a connection error
>
> *** Importing a core ontology -- hope this is okay
> *** Importing terms
> Exception in thread "main" org.biojava.bio.BioException: Error  
> connecting to BioSQL database: Connection is closed.
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:276)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
>  at genevote.BioSQLTest.loadSeq(BioSQLTest.java:31)
>  at genevote.BioSQLTest.main(BioSQLTest.java:70)
> Caused by: java.sql.SQLException: Connection is closed.
>  at org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.checkOpen(PoolingDataSource.java:219)
>  at org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.createStatement(PoolingDataSource.java: 
> 248)
>  at org.biojava.bio.seq.db.biosql.MySQLDBHelper.getInsertID 
> (MySQLDBHelper.java:68)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:268)
>  ... 3 more
>
> Then I tried again, it works, and I put all sequences in genbank  
> format into biosql db without error.
> But, while I tried to extract sequences, exception comes again.
>
> org.biojava.bio.BioException: Error loading ontology terms
>  at org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:444)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.getOntology 
> (OntologySQL.java:116)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.<init> 
> (OntologySQL.java:413)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL 
> (OntologySQL.java:72)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:240)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
>  at genevote.test.loadSeq(test.java:25)
>  at genevote.test.main(test.java:76)
> Caused by: java.sql.SQLException: Unknown column 'name' in 'field  
> list'
>  at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2851)
>  at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1534)
>  at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1625)
>  at com.mysql.jdbc.Connection.execSQL(Connection.java:2297)
>  at com.mysql.jdbc.Connection.execSQL(Connection.java:2226)
>  at com.mysql.jdbc.PreparedStatement.executeInternal 
> (PreparedStatement.java:1812)
>  at com.mysql.jdbc.PreparedStatement.executeQuery 
> (PreparedStatement.java:1657)
>  at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
>  at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms 
> (OntologySQL.java:339)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:441)
>  ... 7 more
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From david at autohandle.com  Wed Jun 21 11:19:28 2006
From: david at autohandle.com (David Scott)
Date: Wed, 21 Jun 2006 08:19:28 -0700
Subject: [BioSQL-l] a biosql/biojavax localization question
Message-ID: <44996380.6060300@autohandle.com>

biojavax is using hibernate to o/r map the biosql database to biojavax 
objects. biojavax is planning support in the biojavax objects for fields 
not directly supported in the biosql database (e.g. isCircular, 
isTaxonHidden). in order to conform to the current biosql database, the 
default mapping file from biosql to biojavax will comment out the 
unsupported fields (so the object fields will not be initialized) and 
the objects will default an appropriate conforming value (e.g. false for 
isCircular and isTaxonHidden). for users wishing to localize biojavax: 
the user would uncomment the mapping file and alter the database tables. 
altering the database would require running ddl on the existing database 
to create the new table columns. what is the best way to review and then 
distribute the alter/create ddl for users to localize their database?

From samuel.thoraval at librophyt.com  Wed Jun 28 08:36:43 2006
From: samuel.thoraval at librophyt.com (Samuel Thoraval)
Date: Wed, 28 Jun 2006 14:36:43 +0200
Subject: [BioSQL-l] BioSQL Schema problem
Message-ID: <44A277DB.6050302@librophyt.com>


Hello,

I am new to biosql and I have 2 problems installing last CVS version 
(*1.4.2.1*, /Sun Jun 16)/:
- running biosqldb-views-pg.sql after biosqldb-pg.sql gives errors, the 
first one being:
psql:biosqldb-views-pg.sql:6: ERROR:  relation "seqfeature_key" does not 
exist
- running load_ncbi_taxonomy.pl with 
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
<ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz> (the script 
download option set to 1 doesn't download anything) gives the following 
error :
----------------------------------------------------------------------------------------------------------------------------------------
 ./scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver Pg --download 0
gunzip: taxdata/taxdump.tar.gz: No such file or directory
tar: taxdump.tar: ne peut open: Aucun fichier ou r?pertoire de ce type
tar: Erreur non r?cup?rable: fin de l'ex?cution imm?diate
Loading NCBI taxon database in taxdata:
        ... retrieving all taxon nodes in the database
        ... reading in taxon nodes from nodes.dmp
        ... insert / update / delete taxon nodes
failed to insert node (1;1;1;no rank;1;0): ERROR:  column "taxon_id" is 
of type integer but expression is of type character varying
HINT:  You will need to rewrite or cast the expression.
----------------------------------------------------------------------------------------------------------------------------------------

The schema expected from the biosqldb-views-pg.sql or taxonomy dump 
file  does not match  the one in biosqldb-pg.sql.


Best regards,

-- 
Samuel Thoraval
LIBROPHYT, Bioinformatique
Centre de Cadarache
B?timent 185, DEVM
13108 St Paul-Lez-Durance
France
T?l:  +33 442 574 799
Fax: +33 442 574 439
e-mail : samuel.thoraval at librophyt.com


From samuel.thoraval at librophyt.com  Wed Jun 28 08:28:21 2006
From: samuel.thoraval at librophyt.com (Samuel Thoraval)
Date: Wed, 28 Jun 2006 14:28:21 +0200
Subject: [BioSQL-l] BioSQL Schema problem
Message-ID: <44A275E5.2040104@librophyt.com>


Hello,

I am new to biosql and I have 2 problems installing last CVS version 
(*1.4.2.1*, /Sun Jun 16)/:
- running biosqldb-views-pg.sql after biosqldb-pg.sql gives errors, the 
first one being:
psql:biosqldb-views-pg.sql:6: ERROR:  relation "seqfeature_key" does not 
exist
- running load_ncbi_taxonomy.pl with 
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
<ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz> (the script 
download option set to 1 doesn't download anything) gives the following 
error :
----------------------------------------------------------------------------------------------------------------------------------------
 ./scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver Pg --download 0
gunzip: taxdata/taxdump.tar.gz: No such file or directory
tar: taxdump.tar: ne peut open: Aucun fichier ou r?pertoire de ce type
tar: Erreur non r?cup?rable: fin de l'ex?cution imm?diate
Loading NCBI taxon database in taxdata:
        ... retrieving all taxon nodes in the database
        ... reading in taxon nodes from nodes.dmp
        ... insert / update / delete taxon nodes
failed to insert node (1;1;1;no rank;1;0): ERROR:  column "taxon_id" is 
of type integer but expression is of type character varying
HINT:  You will need to rewrite or cast the expression.
----------------------------------------------------------------------------------------------------------------------------------------

The schema expected from the biosqldb-views-pg.sql or taxonomy dump 
file  does not match  the one in biosqldb-pg.sql.


Best regards,

-- 
Samuel Thoraval
LIBROPHYT, Bioinformatique
Centre de Cadarache
B?timent 185, DEVM
13108 St Paul-Lez-Durance
France
T?l:  +33 442 574 799
Fax: +33 442 574 439
e-mail : samuel.thoraval at librophyt.com


From petersan at ohsu.edu  Fri Jun 30 18:16:47 2006
From: petersan at ohsu.edu (Sandie Peters)
Date: Fri, 30 Jun 2006 15:16:47 -0700
Subject: [BioSQL-l] Versioning of features
Message-ID: <s4a5406d.040@ohsu.edu>

In the BioSQL v. 1.0 schema overview, the author briefly mentions the possibility of feature set versioning using "dated" source ontology terms.  Has anyone tried this or any other versioning methods with seqfeatures in BioSQL?
 
Thanks,
Sandie Peters
Vollum Institute/OHSU



From d49228002 at ym.edu.tw  Thu Jun  1 13:32:00 2006
From: d49228002 at ym.edu.tw (Yi-Feng Chang)
Date: Thu, 01 Jun 2006 21:32:00 +0800
Subject: [BioSQL-l] Error loading ontology terms
Message-ID: <447EEC50.9090807@ym.edu.tw>

Dear All,
I've checked biosql archives, and found a similar thread
(http://lists.open-bio.org/pipermail/biojava-l/2005-November/005151.html)
however, it did not give specific solution. So I post here again, and
hope there are someone could help me.
I'm using JDK1.5.0_05, Biojava 1.4, Biosql 1.41, and Mysql 5.0 with
My_connectJ 3.1
I was following the demo source that provide by biojava-in-anger except
for the database connection
the exceptions were listed in following:
In first connection there would be a connection error
*** Importing a core ontology -- hope this is okay
*** Importing terms
Exception in thread "main" org.biojava.bio.BioException: Error
connecting to BioSQL database: Connection is closed.
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:276)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:194)
at genevote.BioSQLTest.loadSeq(BioSQLTest.java:31)
at genevote.BioSQLTest.main(BioSQLTest.java:70)
Caused by: java.sql.SQLException: Connection is closed.
at
org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.checkOpen(PoolingDataSource.java:219)
at
org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.createStatement(PoolingDataSource.java:248)
at
org.biojava.bio.seq.db.biosql.MySQLDBHelper.getInsertID(MySQLDBHelper.java:68)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:268)
... 3 more
Then I tried again, it works, and I put all sequences in genbank format
into biosql db without error.
But, while I tried to extract sequences, exception comes again.
org.biojava.bio.BioException: Error loading ontology terms
at
org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology(OntologySQL.java:444)
at
org.biojava.bio.seq.db.biosql.OntologySQL.getOntology(OntologySQL.java:116)
at org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java:413)
at
org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL(OntologySQL.java:72)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:240)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:194)
at genevote.test.loadSeq(test.java:25)
at genevote.test.main(test.java:76)
Caused by: java.sql.SQLException: Unknown column 'name' in 'field list'
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2851)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1534)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1625)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2297)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2226)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1812)
at
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1657)
at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:205)
at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:205)
at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms(OntologySQL.java:339)
at
org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology(OntologySQL.java:441)
... 7 more

yi-feng chang




From d49228002 at ym.edu.tw  Fri Jun  2 06:31:45 2006
From: d49228002 at ym.edu.tw (Yi-Feng Chang)
Date: Fri, 02 Jun 2006 14:31:45 +0800
Subject: [BioSQL-l] [Biojava-l] Error loading ontology terms
In-Reply-To: <447FD342.4090806@uni-tuebingen.de>
References: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
	<1149175573.3948.78.camel@texas.ebi.ac.uk>
	<447FD342.4090806@uni-tuebingen.de>
Message-ID: <447FDB51.9090500@ym.edu.tw>

Thanks, your solution is right.
I solve this problem.
Many thanks.

ian

Andreas Dr?er wrote:
> Hello,
>
> You can solve this problem just by renaming the column "synonym" in
> table "term_synonym" to "name". The reason for changing the name of
> this column is that in some database systems the term "synonym" is a
> reserved word. So the older version that you are using currently might
> cause problems with some databas systems. Once you renamed this
> column, BioJava will work fine.
>
> Andreas Dr?er
>
>> java.sql.SQLException: Unknown column 'name' in 'field list'
>>
>>
>




From andreas.draeger at uni-tuebingen.de  Fri Jun  2 05:57:22 2006
From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=)
Date: Fri, 02 Jun 2006 07:57:22 +0200
Subject: [BioSQL-l] [Biojava-l] Error loading ontology terms
In-Reply-To: <1149175573.3948.78.camel@texas.ebi.ac.uk>
References: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
	<1149175573.3948.78.camel@texas.ebi.ac.uk>
Message-ID: <447FD342.4090806@uni-tuebingen.de>

Hello,

You can solve this problem just by renaming the column "synonym" in 
table "term_synonym" to "name". The reason for changing the name of this 
column is that in some database systems the term "synonym" is a reserved 
word. So the older version that you are using currently might cause 
problems with some databas systems. Once you renamed this column, 
BioJava will work fine.

Andreas Dr?ger

>	java.sql.SQLException: Unknown column 'name' in 'field list'
>  
>

-- 
Dipl.-Bioinform. Andreas Dr?ger
Eberhard Karls University T?bingen
Center for Bioinformatics (ZBIT)
Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091



From richard.holland at ebi.ac.uk  Thu Jun  1 15:26:12 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Thu, 01 Jun 2006 16:26:12 +0100
Subject: [BioSQL-l] Error loading ontology terms
In-Reply-To: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
References: <CE6C8866-E458-4982-BB48-D956AD3CC47F@ym.edu.tw>
Message-ID: <1149175573.3948.78.camel@texas.ebi.ac.uk>

Hi there.

I looked through your stack trace, and the line numbers don't match up
with the current code. I have a strong feeling you may have an out-of-
date version of biojava.

Could you double-check that you have the latest biojava-1.4 version, or
are using the biojava-live version built from CVS?

If you can confirm that you are using the latest 1.4 or biojava-live
then it'd be easier to solve this.

Alternatively, you could have an out-of-date version of the BioSQL
schema. 

The reason I suspect that your BioSQL or BioJava are out of date is
because in the last stack trace you mention, this exception arises:

	java.sql.SQLException: Unknown column 'name' in 'field list'

This shows that BioJava has expected to find a column called 'name' in
some table in BioSQL, but that column is not there. This would only
happen if your BioSQL version did not match the version of BioSQL that
your version of BioJava was expecting.

cheers,
Richard

On Thu, 2006-06-01 at 21:32 +0800, Yi-Feng Chang wrote:
> Leif, this looks more like a biojava or biojava-x related problem, so  
> I'm resending it to the Biojava list. -hilmar
> ======================================================================== 
> ==
> Dear All,
> I've checked biosql archives, and found a similar thread
> (http://lists.open-bio.org/pipermail/biojava-l/2005-November/ 
> 005151.html)
> however, it did not give specific solution. So I post here again, and
> hope there are someone could help me.
> I'm using JDK1.5.0_05, Biojava 1.4, Biosql 1.41, and Mysql 5.0 with
> My_connectJ 3.1
> I was following the demo source that provide by biojava-in-anger except
> for the database connection
> the exceptions were listed in following:
> In first connection there would be a connection error
> *** Importing a core ontology -- hope this is okay
> *** Importing terms
> Exception in thread "main" org.biojava.bio.BioException: Error
> connecting to BioSQL database: Connection is closed.
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:276)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
> at genevote.BioSQLTest.loadSeq(BioSQLTest.java:31)
> at genevote.BioSQLTest.main(BioSQLTest.java:70)
> Caused by: java.sql.SQLException: Connection is closed.
> at
> org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.checkOpen(PoolingDataSource.java:219)
> at
> org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.createStatement(PoolingDataSource.java:248)
> at
> org.biojava.bio.seq.db.biosql.MySQLDBHelper.getInsertID 
> (MySQLDBHelper.java:68)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:268)
> ... 3 more
> Then I tried again, it works, and I put all sequences in genbank format
> into biosql db without error.
> But, while I tried to extract sequences, exception comes again.
> org.biojava.bio.BioException: Error loading ontology terms
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:444)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.getOntology 
> (OntologySQL.java:116)
> at org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java: 
> 413)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL 
> (OntologySQL.java:72)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:240)
> at
> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
> at genevote.test.loadSeq(test.java:25)
> at genevote.test.main(test.java:76)
> Caused by: java.sql.SQLException: Unknown column 'name' in 'field list'
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2851)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1534)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1625)
> at com.mysql.jdbc.Connection.execSQL(Connection.java:2297)
> at com.mysql.jdbc.Connection.execSQL(Connection.java:2226)
> at
> com.mysql.jdbc.PreparedStatement.executeInternal 
> (PreparedStatement.java:1812)
> at
> com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java: 
> 1657)
> at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
> at
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
> at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms 
> (OntologySQL.java:339)
> at
> org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:441)
> ... 7 more
> 
> yi-feng chang
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416



From n.saunders at uq.edu.au  Tue Jun  6 05:41:34 2006
From: n.saunders at uq.edu.au (Neil Saunders)
Date: Tue, 06 Jun 2006 15:41:34 +1000
Subject: [BioSQL-l] Problem loading GenPept files into mysql biosql
Message-ID: <4485158E.2010202@uq.edu.au>

hi,

I've installed the MySQL BioSQL schema (Ubuntu Linux 5.10, BioPerl 1.5, MySQL 
4.1.12).  I have written a script that uses Bio::DB::GenPept to retrieve files 
by GI and then tries to load them using load_seqdatabase.pl:

load_seqdatabase.pl --safe --dbname DBNAME --dbuser DBUSER --dbpass DBPASS 
--namespace genpept --format genbank <files>

I'm getting a lot of errors of type:

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were 
("","Direct Submission","Submitted (11-SEP-2004) National Center for 
Biotechnology Information, NIH, Bethesda, MD 20894, 
USA","CRC-EFE0D20CE0E07E7D","1","637","") FKs (<NULL>)
Duplicate entry 'CRC-EFE0D20CE0E07E7D' for key 3
---------------------------------------------------

This seems to be related to a similar problem using UniProt discussed on this list:

http://lists.open-bio.org/pipermail/biosql-l/2006-May/000977.html

Am I right in thinking that a CRC is generated from the JOURNAL line of a 
GenPept file and that non-unique CRCs are causing this problem?  My GenPept 
files are actually RefSeq entries from complete microbial genomes.  An example 
would be NP_378145 (GI 15922476).  The REFERENCE for such records is often 
"Direct Submission" rather than a journal and obviously in these cases, the set 
of all proteins from a genome has the same REFERENCE, so unique CRCs don't seem 
like a good idea.

I'd be grateful if anyone could confirm that these records are a problem and 
suggest any workarounds,

thanks,
Neil
-- 
  School of Molecular and Microbial Sciences
  University of Queensland
  Brisbane 4072 Australia

http://psychro.bioinformatics.unsw.edu.au/neil


From cjfields at uiuc.edu  Tue Jun  6 14:49:15 2006
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 6 Jun 2006 09:49:15 -0500
Subject: [BioSQL-l] Problem loading GenPept files into mysql biosql
In-Reply-To: <4485158E.2010202@uq.edu.au>
Message-ID: <000b01c68978$620a2270$15327e82@pyrimidine>

I had similar issues with these files.  Hilmar had this to say in a previous
post to bioperl-l:

http://article.gmane.org/gmane.comp.lang.perl.bio.general/10068

> I would generally advise against taking Uniprot/Swissprot entries from
> their GenPept reincarnation. The formats are incompatible in some
> aspects (e.g., Swissprot, like EMBL, has first-level db_xrefs, whereas
> GenBank format doesn't; instead it puts db_xrefs into the feature
> table).

If you really need these sequences, you should probably grab them from
UniProt/SwissProt directly and use 'swiss' Bio::SeqIO format.  I never found
a use for them since there was normally a properly-parsed GenBank
counterpart (though I hate the fact that they seemingly clog up the works).
We probably should have some warning added for these sequences in bioperl or
bioperl-db if this keeps popping up, though.

Chris

> -----Original Message-----
> From: biosql-l-bounces at lists.open-bio.org [mailto:biosql-l-
> bounces at lists.open-bio.org] On Behalf Of Neil Saunders
> Sent: Tuesday, June 06, 2006 12:42 AM
> To: biosql-l at lists.open-bio.org
> Subject: [BioSQL-l] Problem loading GenPept files into mysql biosql
> 
> hi,
> 
> I've installed the MySQL BioSQL schema (Ubuntu Linux 5.10, BioPerl 1.5,
> MySQL
> 4.1.12).  I have written a script that uses Bio::DB::GenPept to retrieve
> files
> by GI and then tries to load them using load_seqdatabase.pl:
> 
> load_seqdatabase.pl --safe --dbname DBNAME --dbuser DBUSER --dbpass DBPASS
> --namespace genpept --format genbank <files>
> 
> I'm getting a lot of errors of type:
> 
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values
> were
> ("","Direct Submission","Submitted (11-SEP-2004) National Center for
> Biotechnology Information, NIH, Bethesda, MD 20894,
> USA","CRC-EFE0D20CE0E07E7D","1","637","") FKs (<NULL>)
> Duplicate entry 'CRC-EFE0D20CE0E07E7D' for key 3
> ---------------------------------------------------
> 
> This seems to be related to a similar problem using UniProt discussed on
> this list:
> 
> http://lists.open-bio.org/pipermail/biosql-l/2006-May/000977.html
> 
> Am I right in thinking that a CRC is generated from the JOURNAL line of a
> GenPept file and that non-unique CRCs are causing this problem?  My
> GenPept
> files are actually RefSeq entries from complete microbial genomes.  An
> example
> would be NP_378145 (GI 15922476).  The REFERENCE for such records is often
> "Direct Submission" rather than a journal and obviously in these cases,
> the set
> of all proteins from a genome has the same REFERENCE, so unique CRCs don't
> seem
> like a good idea.
> 
> I'd be grateful if anyone could confirm that these records are a problem
> and
> suggest any workarounds,
> 
> thanks,
> Neil
> --
>   School of Molecular and Microbial Sciences
>   University of Queensland
>   Brisbane 4072 Australia
> 
> http://psychro.bioinformatics.unsw.edu.au/neil
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l



From hlapp at gmx.net  Wed Jun  7 12:52:22 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 7 Jun 2006 08:52:22 -0400
Subject: [BioSQL-l] [Bioperl-l] bioperl-db failing tests
In-Reply-To: <2000234931344D4BA434A0C235D1956B0C4852@hsv-exmail02.operonads.local>
References: <2000234931344D4BA434A0C235D1956B0C4852@hsv-exmail02.operonads.local>
Message-ID: <4F23D2EA-2218-4023-A3F6-3284912952BE@gmx.net>

Hi Michael,

Bioperl-db will open all connections with AutoCommit => 0 in the DBI  
parameter hash. The test you're stumbling over is actually there to  
test that the database  does support transactions, but apparently in  
5.x versions MySQL no longer silently ignores the AutoCommit  
parameter if it doesn't support transactions (effectively preempting  
the test ...).

Now you say that innodb shows as enabled - i.e., you can confirm that  
you changed the Mysql configuration parameter that designates the  
directory for innodb to store its files?

You can confirm that transactions are supported by simple tests on  
the sql level. Open a mysql shell and do the following:

	-- BTW 'start transaction;' will (should) work too
	mysql> set autocommit = 0;
	mysql> insert into biodatabase (name) values ('__dummy__');
	mysql> select name from biodatabase where name = '__dummy__';
	mysql> rollback;
	mysql> select name from biodatabase where name = '__dummy__';

The first SELECT query should return one and the last query should  
return zero rows if transactions are supported, and there shouldn't  
be any error.

If the above succeeds (which I don't expect it to) then it looks like  
the DBD::mysql driver thinks the database doesn't support  
transactions when in reality it does. Let me know the result.

	-hilmar

On Jun 6, 2006, at 2:34 PM, Michael Muratet US-Huntsville wrote:

> Greetings
>
> I am trying to install bioperl-db in preparation for installing a  
> biosql database. I'm running on a Dell PowerEdge with quad dual- 
> core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl  
> 1.5.1.  I have installed mysql v5.0.21 from source with --with- 
> innodb set for the configuration. I installed bioperl-db from cvs.  
> I have the latest DBI and DBD:mysql installed a few weeks ago from  
> CPAN. The installation has been working well with perl otherwise,  
> for example, the Ensembl core API works OK. SHOW ENGINES indicates  
> that innodb is enabled.  I have attached a snippet from the top of  
> the output below. I searched the web and the bioperl-db list and  
> haven't found anything that appears to be relevant. I've done  
> several of these installs and they've pretty much completed without  
> a single glitch. Does anyone have any ideas how to isolate the  
> problem?
>
> Thanks
>
> Mike
>
> [mmuratet at HSV-PROBE bioperl-db]$ make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"  
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/01dbadaptor.....ok 14/19
> ------------- EXCEPTION  -------------
> MSG: failed to open connection: Transactions not supported by database
> STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:255
> STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:215
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/ 
> site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/ 
> BioSQL/BasePersistenceAdaptor.pm:1477
> STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/ 
> perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/ 
> DB/BioSQL/BaseDriver.pm:518
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
> STACK toplevel t/01dbadaptor.t:62
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From Michael.Muratet at operon.com  Tue Jun  6 18:34:38 2006
From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville)
Date: Tue, 6 Jun 2006 13:34:38 -0500
Subject: [BioSQL-l] bioperl-db failing tests
Message-ID: <2000234931344D4BA434A0C235D1956B0C4852@hsv-exmail02.operonads.local>

Greetings

I am trying to install bioperl-db in preparation for installing a biosql database. I'm running on a Dell PowerEdge with quad dual-core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl 1.5.1.  I have installed mysql v5.0.21 from source with --with-innodb set for the configuration. I installed bioperl-db from cvs. I have the latest DBI and DBD:mysql installed a few weeks ago from CPAN. The installation has been working well with perl otherwise, for example, the Ensembl core API works OK. SHOW ENGINES indicates that innodb is enabled.  I have attached a snippet from the top of the output below. I searched the web and the bioperl-db list and haven't found anything that appears to be relevant. I've done several of these installs and they've pretty much completed without a single glitch. Does anyone have any ideas how to isolate the problem?

Thanks

Mike

[mmuratet at HSV-PROBE bioperl-db]$ make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01dbadaptor.....ok 14/19
------------- EXCEPTION  -------------
MSG: failed to open connection: Transactions not supported by database
STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:255
STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:215
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1477
STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BaseDriver.pm:518
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
STACK toplevel t/01dbadaptor.t:62




From david at autohandle.com  Wed Jun  7 15:45:41 2006
From: david at autohandle.com (David Scott)
Date: Wed, 07 Jun 2006 08:45:41 -0700
Subject: [BioSQL-l] value field in seqfeature_qualifier_value too small
Message-ID: <4486F4A5.3010602@autohandle.com>

in seqfeature_qualifier_value:
 
  SEQFEATURE_ID                             NOT NULL NUMBER(38)
  TERM_ID                                   NOT NULL NUMBER(38)
  RANK                                      NOT NULL NUMBER(3)
  VALUE                                              VARCHAR2(4000)
 
 the value field is restricted to 4000 bytes - 4000 bytes too small to 
 carry current genbank protein translations - e.g. AB016240.1 has a 
 protein translation of 4133 characters. since 4000 bytes is a string 
 length restriction for some jdbc drivers - to increase the field size, 
 the field type should also be changed to clob.



From hlapp at gmx.net  Wed Jun  7 17:15:49 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 7 Jun 2006 13:15:49 -0400
Subject: [BioSQL-l] value field in seqfeature_qualifier_value too small
In-Reply-To: <4486F4A5.3010602@autohandle.com>
References: <4486F4A5.3010602@autohandle.com>
Message-ID: <39531248-B1A0-4911-9F4A-6D97D050B0A3@gmx.net>

You may make this change in your installation, and I should maybe  
document this possibility in the schema.

However, there are some serious issues with doing so. First off, you  
will no longer be able to search by simple query (you'd have to use  
DBMS_LOB functions), and you can't index the column any more.  
Furthermore, all language bindings will need special code to use the  
stream or other LOB API for getting/setting the value. There's  
additional issues that LOB columns raise compared to VARCHAR types.

It's worth noting that this applies so far only to Oracle (the other  
RDBMSs do not impose the length restriction), and it's in reality  
only the value of the protein translation feature tag that exceeds  
the limit on occasion.

I personally strip the protein translation tag from all loaded  
Genbank and RefSeq records because the value may be computed easily  
on the fly, and the respective sequences are usually there too unless  
you don't load Genpept or the NP_/XP_* part of RefSeq - but in this  
case I don't understand why you would want the tag value but not the  
full sequence.

Not the easy answer you may have hoped for, and I'd welcome any  
suggestions for how the problem could be solved w/o using CLOBs.

	-hilmar

On Jun 7, 2006, at 11:45 AM, David Scott wrote:

> in seqfeature_qualifier_value:
>
>   SEQFEATURE_ID                             NOT NULL NUMBER(38)
>   TERM_ID                                   NOT NULL NUMBER(38)
>   RANK                                      NOT NULL NUMBER(3)
>   VALUE                                              VARCHAR2(4000)
>
>  the value field is restricted to 4000 bytes - 4000 bytes too small to
>  carry current genbank protein translations - e.g. AB016240.1 has a
>  protein translation of 4133 characters. since 4000 bytes is a string
>  length restriction for some jdbc drivers - to increase the field  
> size,
>  the field type should also be changed to clob.
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From hlapp at gmx.net  Wed Jun  7 17:25:25 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 7 Jun 2006 13:25:25 -0400
Subject: [BioSQL-l] [Bioperl-l] bioperl-db failing tests
In-Reply-To: <2000234931344D4BA434A0C235D1956B0C485C@hsv-exmail02.operonads.local>
References: <2000234931344D4BA434A0C235D1956B0C485C@hsv-exmail02.operonads.local>
Message-ID: <76434774-51A4-46E7-97AA-1E9227CB7771@gmx.net>

Hi Michael,

yes it looks like a problem in DBD if DBD::mysql fails to recognize  
that the mysql instance to which it is connected does support  
transactions. You can verify this by writing a simple script that  
tries to open a connection with
{ AutoCommit => 0 } as the parameter hash:

	use DBI;
	my $dbh = DBI->connect("dbi:mysql:database=<yourdb>;host=<yourhost>",
	                       "username","password",
	                       { AutoCommit => 0, RaiseError => 0 });
	die DBI::errstr unless $dbh;
	$dbh->disconnect;

If this succeeds fine then something in Biosql may be related to the  
problem, but otherwise not.

	-hilmar


On Jun 7, 2006, at 12:01 PM, Michael Muratet US-Huntsville wrote:

> Hilmar
>
> Pardon the top post.
>
> I tried the test below and it failed. So, I went back and redid the  
> Innodb configuration (deleted all the index files--they were empty  
> anyway, reinstalled biosql (which was empty,too) and restarted the  
> server. Now, the test below works. I went into the DBD-3.0003 and  
> did a distclean and reinstalled the package, but it fails the one  
> transaction test, too. So, it looks like the problem is in DBD, yes?
>
> We had a RAID 5 drive glitch the day before yesterday and rebuilt  
> it. That's the only thing that's changed that I know of that could  
> have caused the problem with ibxxx files.
>
> I have received a reply on the DBD list. Can you think of anything  
> else I should try from the biosql end?
>
> Thanks a million.
>
> Mike
>
> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Wednesday, June 07, 2006 7:52 AM
> To: Michael Muratet US-Huntsville
> Cc: Bioperl; BioSQL
> Subject: Re: [Bioperl-l] bioperl-db failing tests
>
>
> Hi Michael,
>
> Bioperl-db will open all connections with AutoCommit => 0 in the DBI
> parameter hash. The test you're stumbling over is actually there to
> test that the database  does support transactions, but apparently in
> 5.x versions MySQL no longer silently ignores the AutoCommit
> parameter if it doesn't support transactions (effectively preempting
> the test ...).
>
> Now you say that innodb shows as enabled - i.e., you can confirm that
> you changed the Mysql configuration parameter that designates the
> directory for innodb to store its files?
>
> You can confirm that transactions are supported by simple tests on
> the sql level. Open a mysql shell and do the following:
>
> 	-- BTW 'start transaction;' will (should) work too
> 	mysql> set autocommit = 0;
> 	mysql> insert into biodatabase (name) values ('__dummy__');
> 	mysql> select name from biodatabase where name = '__dummy__';
> 	mysql> rollback;
> 	mysql> select name from biodatabase where name = '__dummy__';
>
> The first SELECT query should return one and the last query should
> return zero rows if transactions are supported, and there shouldn't
> be any error.
>
> If the above succeeds (which I don't expect it to) then it looks like
> the DBD::mysql driver thinks the database doesn't support
> transactions when in reality it does. Let me know the result.
>
> 	-hilmar
>
> On Jun 6, 2006, at 2:34 PM, Michael Muratet US-Huntsville wrote:
>
>> Greetings
>>
>> I am trying to install bioperl-db in preparation for installing a
>> biosql database. I'm running on a Dell PowerEdge with quad dual-
>> core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl
>> 1.5.1.  I have installed mysql v5.0.21 from source with --with-
>> innodb set for the configuration. I installed bioperl-db from cvs.
>> I have the latest DBI and DBD:mysql installed a few weeks ago from
>> CPAN. The installation has been working well with perl otherwise,
>> for example, the Ensembl core API works OK. SHOW ENGINES indicates
>> that innodb is enabled.  I have attached a snippet from the top of
>> the output below. I searched the web and the bioperl-db list and
>> haven't found anything that appears to be relevant. I've done
>> several of these installs and they've pretty much completed without
>> a single glitch. Does anyone have any ideas how to isolate the
>> problem?
>>
>> Thanks
>>
>> Mike
>>
>> [mmuratet at HSV-PROBE bioperl-db]$ make test
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>> t/01dbadaptor.....ok 14/19
>> ------------- EXCEPTION  -------------
>> MSG: failed to open connection: Transactions not supported by  
>> database
>> STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/
>> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm: 
>> 255
>> STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/
>> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm: 
>> 215
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/
>> site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/
>> BioSQL/BasePersistenceAdaptor.pm:1477
>> STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/
>> perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/
>> DB/BioSQL/BaseDriver.pm:518
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /
>> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/
>> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /
>> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/
>> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
>> STACK toplevel t/01dbadaptor.t:62
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From Michael.Muratet at operon.com  Wed Jun  7 16:01:29 2006
From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville)
Date: Wed, 7 Jun 2006 11:01:29 -0500
Subject: [BioSQL-l] [Bioperl-l] bioperl-db failing tests
Message-ID: <2000234931344D4BA434A0C235D1956B0C485C@hsv-exmail02.operonads.local>

Hilmar

Pardon the top post.

I tried the test below and it failed. So, I went back and redid the Innodb configuration (deleted all the index files--they were empty anyway, reinstalled biosql (which was empty,too) and restarted the server. Now, the test below works. I went into the DBD-3.0003 and did a distclean and reinstalled the package, but it fails the one transaction test, too. So, it looks like the problem is in DBD, yes?

We had a RAID 5 drive glitch the day before yesterday and rebuilt it. That's the only thing that's changed that I know of that could have caused the problem with ibxxx files. 

I have received a reply on the DBD list. Can you think of anything else I should try from the biosql end?

Thanks a million.

Mike

-----Original Message-----
From: Hilmar Lapp [mailto:hlapp at gmx.net]
Sent: Wednesday, June 07, 2006 7:52 AM
To: Michael Muratet US-Huntsville
Cc: Bioperl; BioSQL
Subject: Re: [Bioperl-l] bioperl-db failing tests


Hi Michael,

Bioperl-db will open all connections with AutoCommit => 0 in the DBI  
parameter hash. The test you're stumbling over is actually there to  
test that the database  does support transactions, but apparently in  
5.x versions MySQL no longer silently ignores the AutoCommit  
parameter if it doesn't support transactions (effectively preempting  
the test ...).

Now you say that innodb shows as enabled - i.e., you can confirm that  
you changed the Mysql configuration parameter that designates the  
directory for innodb to store its files?

You can confirm that transactions are supported by simple tests on  
the sql level. Open a mysql shell and do the following:

	-- BTW 'start transaction;' will (should) work too
	mysql> set autocommit = 0;
	mysql> insert into biodatabase (name) values ('__dummy__');
	mysql> select name from biodatabase where name = '__dummy__';
	mysql> rollback;
	mysql> select name from biodatabase where name = '__dummy__';

The first SELECT query should return one and the last query should  
return zero rows if transactions are supported, and there shouldn't  
be any error.

If the above succeeds (which I don't expect it to) then it looks like  
the DBD::mysql driver thinks the database doesn't support  
transactions when in reality it does. Let me know the result.

	-hilmar

On Jun 6, 2006, at 2:34 PM, Michael Muratet US-Huntsville wrote:

> Greetings
>
> I am trying to install bioperl-db in preparation for installing a  
> biosql database. I'm running on a Dell PowerEdge with quad dual- 
> core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl  
> 1.5.1.  I have installed mysql v5.0.21 from source with --with- 
> innodb set for the configuration. I installed bioperl-db from cvs.  
> I have the latest DBI and DBD:mysql installed a few weeks ago from  
> CPAN. The installation has been working well with perl otherwise,  
> for example, the Ensembl core API works OK. SHOW ENGINES indicates  
> that innodb is enabled.  I have attached a snippet from the top of  
> the output below. I searched the web and the bioperl-db list and  
> haven't found anything that appears to be relevant. I've done  
> several of these installs and they've pretty much completed without  
> a single glitch. Does anyone have any ideas how to isolate the  
> problem?
>
> Thanks
>
> Mike
>
> [mmuratet at HSV-PROBE bioperl-db]$ make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"  
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/01dbadaptor.....ok 14/19
> ------------- EXCEPTION  -------------
> MSG: failed to open connection: Transactions not supported by database
> STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:255
> STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/ 
> 5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:215
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/ 
> site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/ 
> BioSQL/BasePersistenceAdaptor.pm:1477
> STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/ 
> perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/ 
> DB/BioSQL/BaseDriver.pm:518
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key / 
> usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/ 
> lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
> STACK toplevel t/01dbadaptor.t:62
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================








From hlapp at gmx.net  Sun Jun 11 03:45:01 2006
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 10 Jun 2006 23:45:01 -0400
Subject: [BioSQL-l] Error loading ontology terms
In-Reply-To: <000001c68c97$f461ac70$6801a8c0@iannb>
References: <000001c68c97$f461ac70$6801a8c0@iannb>
Message-ID: <90FF3359-AA97-4F6D-9A7D-8AA8E0590A10@gmx.net>

The specific solution is in the biojava list archives, not the biosql  
list. If I remember correctly, you need to either upgrade biojava or  
biosql or both to the latest revision.

	-hilmar

On May 31, 2006, at 10:39 AM, Yi-Feng Chang wrote:

> Dear All,
> I've checked biosql archives, and found a similar thread (http:// 
> lists.open-bio.org/pipermail/biojava-l/2005-November/005151.html)  
> however, it did not give specific solution. So I post here again,  
> and hope there are someone could help me.
> I'm using JDK1.5.0_05, Biojava 1.4, Biosql 1.41, and Mysql 5.0 with  
> My_connectJ 3.1
>
> I was following the demo source that provide by biojava-in-anger  
> except for the database connection
> the exceptions were listed in following:
>
> In first connection there would be a connection error
>
> *** Importing a core ontology -- hope this is okay
> *** Importing terms
> Exception in thread "main" org.biojava.bio.BioException: Error  
> connecting to BioSQL database: Connection is closed.
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:276)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
>  at genevote.BioSQLTest.loadSeq(BioSQLTest.java:31)
>  at genevote.BioSQLTest.main(BioSQLTest.java:70)
> Caused by: java.sql.SQLException: Connection is closed.
>  at org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.checkOpen(PoolingDataSource.java:219)
>  at org.apache.commons.dbcp.PoolingDataSource 
> $PoolGuardConnectionWrapper.createStatement(PoolingDataSource.java: 
> 248)
>  at org.biojava.bio.seq.db.biosql.MySQLDBHelper.getInsertID 
> (MySQLDBHelper.java:68)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:268)
>  ... 3 more
>
> Then I tried again, it works, and I put all sequences in genbank  
> format into biosql db without error.
> But, while I tried to extract sequences, exception comes again.
>
> org.biojava.bio.BioException: Error loading ontology terms
>  at org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:444)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.getOntology 
> (OntologySQL.java:116)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.<init> 
> (OntologySQL.java:413)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL 
> (OntologySQL.java:72)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb 
> (BioSQLSequenceDB.java:240)
>  at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init> 
> (BioSQLSequenceDB.java:194)
>  at genevote.test.loadSeq(test.java:25)
>  at genevote.test.main(test.java:76)
> Caused by: java.sql.SQLException: Unknown column 'name' in 'field  
> list'
>  at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2851)
>  at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1534)
>  at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1625)
>  at com.mysql.jdbc.Connection.execSQL(Connection.java:2297)
>  at com.mysql.jdbc.Connection.execSQL(Connection.java:2226)
>  at com.mysql.jdbc.PreparedStatement.executeInternal 
> (PreparedStatement.java:1812)
>  at com.mysql.jdbc.PreparedStatement.executeQuery 
> (PreparedStatement.java:1657)
>  at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
>  at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery 
> (DelegatingPreparedStatement.java:205)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.loadTerms 
> (OntologySQL.java:339)
>  at org.biojava.bio.seq.db.biosql.OntologySQL.loadOntology 
> (OntologySQL.java:441)
>  ... 7 more
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From david at autohandle.com  Wed Jun 21 15:19:28 2006
From: david at autohandle.com (David Scott)
Date: Wed, 21 Jun 2006 08:19:28 -0700
Subject: [BioSQL-l] a biosql/biojavax localization question
Message-ID: <44996380.6060300@autohandle.com>

biojavax is using hibernate to o/r map the biosql database to biojavax 
objects. biojavax is planning support in the biojavax objects for fields 
not directly supported in the biosql database (e.g. isCircular, 
isTaxonHidden). in order to conform to the current biosql database, the 
default mapping file from biosql to biojavax will comment out the 
unsupported fields (so the object fields will not be initialized) and 
the objects will default an appropriate conforming value (e.g. false for 
isCircular and isTaxonHidden). for users wishing to localize biojavax: 
the user would uncomment the mapping file and alter the database tables. 
altering the database would require running ddl on the existing database 
to create the new table columns. what is the best way to review and then 
distribute the alter/create ddl for users to localize their database?


From samuel.thoraval at librophyt.com  Wed Jun 28 12:36:43 2006
From: samuel.thoraval at librophyt.com (Samuel Thoraval)
Date: Wed, 28 Jun 2006 14:36:43 +0200
Subject: [BioSQL-l] BioSQL Schema problem
Message-ID: <44A277DB.6050302@librophyt.com>


Hello,

I am new to biosql and I have 2 problems installing last CVS version 
(*1.4.2.1*, /Sun Jun 16)/:
- running biosqldb-views-pg.sql after biosqldb-pg.sql gives errors, the 
first one being:
psql:biosqldb-views-pg.sql:6: ERROR:  relation "seqfeature_key" does not 
exist
- running load_ncbi_taxonomy.pl with 
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
<ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz> (the script 
download option set to 1 doesn't download anything) gives the following 
error :
----------------------------------------------------------------------------------------------------------------------------------------
 ./scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver Pg --download 0
gunzip: taxdata/taxdump.tar.gz: No such file or directory
tar: taxdump.tar: ne peut open: Aucun fichier ou r?pertoire de ce type
tar: Erreur non r?cup?rable: fin de l'ex?cution imm?diate
Loading NCBI taxon database in taxdata:
        ... retrieving all taxon nodes in the database
        ... reading in taxon nodes from nodes.dmp
        ... insert / update / delete taxon nodes
failed to insert node (1;1;1;no rank;1;0): ERROR:  column "taxon_id" is 
of type integer but expression is of type character varying
HINT:  You will need to rewrite or cast the expression.
----------------------------------------------------------------------------------------------------------------------------------------

The schema expected from the biosqldb-views-pg.sql or taxonomy dump 
file  does not match  the one in biosqldb-pg.sql.


Best regards,

-- 
Samuel Thoraval
LIBROPHYT, Bioinformatique
Centre de Cadarache
B?timent 185, DEVM
13108 St Paul-Lez-Durance
France
T?l:  +33 442 574 799
Fax: +33 442 574 439
e-mail : samuel.thoraval at librophyt.com



From samuel.thoraval at librophyt.com  Wed Jun 28 12:28:21 2006
From: samuel.thoraval at librophyt.com (Samuel Thoraval)
Date: Wed, 28 Jun 2006 14:28:21 +0200
Subject: [BioSQL-l] BioSQL Schema problem
Message-ID: <44A275E5.2040104@librophyt.com>


Hello,

I am new to biosql and I have 2 problems installing last CVS version 
(*1.4.2.1*, /Sun Jun 16)/:
- running biosqldb-views-pg.sql after biosqldb-pg.sql gives errors, the 
first one being:
psql:biosqldb-views-pg.sql:6: ERROR:  relation "seqfeature_key" does not 
exist
- running load_ncbi_taxonomy.pl with 
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
<ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz> (the script 
download option set to 1 doesn't download anything) gives the following 
error :
----------------------------------------------------------------------------------------------------------------------------------------
 ./scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver Pg --download 0
gunzip: taxdata/taxdump.tar.gz: No such file or directory
tar: taxdump.tar: ne peut open: Aucun fichier ou r?pertoire de ce type
tar: Erreur non r?cup?rable: fin de l'ex?cution imm?diate
Loading NCBI taxon database in taxdata:
        ... retrieving all taxon nodes in the database
        ... reading in taxon nodes from nodes.dmp
        ... insert / update / delete taxon nodes
failed to insert node (1;1;1;no rank;1;0): ERROR:  column "taxon_id" is 
of type integer but expression is of type character varying
HINT:  You will need to rewrite or cast the expression.
----------------------------------------------------------------------------------------------------------------------------------------

The schema expected from the biosqldb-views-pg.sql or taxonomy dump 
file  does not match  the one in biosqldb-pg.sql.


Best regards,

-- 
Samuel Thoraval
LIBROPHYT, Bioinformatique
Centre de Cadarache
B?timent 185, DEVM
13108 St Paul-Lez-Durance
France
T?l:  +33 442 574 799
Fax: +33 442 574 439
e-mail : samuel.thoraval at librophyt.com



From petersan at ohsu.edu  Fri Jun 30 22:16:47 2006
From: petersan at ohsu.edu (Sandie Peters)
Date: Fri, 30 Jun 2006 15:16:47 -0700
Subject: [BioSQL-l] Versioning of features
Message-ID: <s4a5406d.040@ohsu.edu>

In the BioSQL v. 1.0 schema overview, the author briefly mentions the possibility of feature set versioning using "dated" source ontology terms.  Has anyone tried this or any other versioning methods with seqfeatures in BioSQL?
 
Thanks,
Sandie Peters
Vollum Institute/OHSU