From ekabore at irisa.fr  Wed Dec  3 08:04:46 2003
From: ekabore at irisa.fr (Esther Kabore)
Date: Wed Dec  3 08:11:01 2003
Subject: [BioSQL-l] Troubles with load_seqdatabase.pl
References: <200311141633.hAEGXScm024011@portal.open-bio.org>
Message-ID: <3FCDDF6E.3080102@irisa.fr>


Hi,
when trying to load data in my PostgreS database through 
load-seqdatabase.pl, I get this error message:

Can't locate object method "category" via package "Bio::Annotation::OntologyTerm" at /local/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm line 488, <GEN0> line 1015.

I use --lookup and --safe options.
Thank you for helping me.
Esther

From hlapp at gnf.org  Wed Dec  3 20:10:45 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Dec  3 20:17:05 2003
Subject: [BioSQL-l] Troubles with load_seqdatabase.pl
Message-ID: <833E32F61B9F8746878F2A1865BECE60430997@EXCHCLUSTER01.lj.gnf.org>

This sounds like a bioperl version mismatch problem. Which version of
bioperl are you running? You'll need at least 1.2.3 installed.

	-hilmar

> -----Original Message-----
> From: Esther Kabore [mailto:ekabore@irisa.fr] 
> Sent: Wednesday, December 03, 2003 5:05 AM
> To: biosql-l@portal.open-bio.org
> Subject: [BioSQL-l] Troubles with load_seqdatabase.pl
> 
> 
> 
> Hi,
> when trying to load data in my PostgreS database through 
> load-seqdatabase.pl, I get this error message:
> 
> Can't locate object method "category" via package 
> "Bio::Annotation::OntologyTerm" at 
> /local/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentO
> bject.pm line 488, <GEN0> line 1015.
> 
> I use --lookup and --safe options.
> Thank you for helping me.
> Esther
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l@open-bio.org http://open-bio.org/mailman/listinfo/biosql-l
> 

From christen at unice.fr  Mon Dec  8 08:57:32 2003
From: christen at unice.fr (christen)
Date: Mon Dec  8 09:02:08 2003
Subject: [BioSQL-l] python
Message-ID: <012101c3bd93$39ee0c10$2b113b86@christen2002>

Hi there

I am a new comer to python and biosql

I have tried to get working biosql under mysql and python as ewplained in
Basic BioSQL with Biopoython
I have donwloaded the latest version of both, and tried the example with
cor6_6.gb

then I got numerous problems

I fixed the first one by changing line 104 in cursors from
            if args is None:
to :
            if args is None or args=='':

then in Loader, in def _load_reference(self, reference, rank, bioentry_id):,
i made the following changes (in particular replaced JOIN by INNER JOIN)
if reference.medline_id:
            sql="SELECT reference_id" \
                "  FROM reference INNER JOIN dbxref ON reference .dbxref_id
= dbxref.dbxref_id" \
                " WHERE ((dbname = 'MEDLINE') AND (accession = %s))"
            refs =
self.adaptor.execute_and_fetch_col0(sql,reference.medline_id)


Now, I have one more pb:

Traceback (most recent call last):
  File "C:\Python23\RC_databases\rc_BioSQL_GenBank.py", line 21,
in -toplevel-
    db.load(iterator)
  File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 343,
in load
    db_loader.load_seqrecord(cur_record)
  File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 46, in
load_seqrecord
    self._load_seqfeature(seq_feature, seq_feature_num, bioentry_id)
  File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 366, in
_load_seqfeature
    self._load_seqfeature_locations(feature, seqfeature_id)
  File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 409, in
_load_seqfeature_locations
    self._insert_seqfeature_location(feature, 1, seqfeature_id)
  File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 430, in
_insert_seqfeature_location
    self.adaptor.execute(sql, (seqfeature_id, start, end, strand, rank))
  File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 223,
in execute
    self.cursor.execute(sql, args)
  File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 95, in
execute
    return self._execute(query, args)
  File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 119, in
_execute
    self.errorhandler(self, exc, value)
  File "C:\Python23\Lib\site-packages\MySQLdb\connections.py", line 33, in
defaulterrorhandler
    raise errorclass, errorvalue
OperationalError: (1048, "Le champ 'strand' ne peut \xeatre vide (null)")


I am for the time being only trying some quick and dirty (like modification
of cursor instead of loader I guess...) changes  to try to get it working
My questions are :
Is there somebody else having trouble, or do you I miss something ?
If I did it right, Is there somebody else trying to fix these problems ?
If things need some help, it would be very nice to have some clear
description of biosql structure. I have not been able to find it. Somebody
could help ?

thanks in advance





Richard CHRISTEN
Champion de saut en largeur
UMR6543 CNRS - Universit? de Nice Sophia Antipolis

Centre de Biochimie
Parc Valrose
06108 Nice cedex2

tel  33 - 492 076 947
fax 33 - 492 076 408

From Yves.Bastide at irisa.fr  Mon Dec  8 09:47:53 2003
From: Yves.Bastide at irisa.fr (Yves Bastide)
Date: Mon Dec  8 09:54:02 2003
Subject: [BioSQL-l] python
In-Reply-To: <012101c3bd93$39ee0c10$2b113b86@christen2002>
References: <012101c3bd93$39ee0c10$2b113b86@christen2002>
Message-ID: <3FD48F19.6040403@irisa.fr>

[kept bioSQL cc'ed, f'up to biopython-dev@biopython.org]

christen wrote:
> Hi there
> 
> I am a new comer to python and biosql
> 
> I have tried to get working biosql under mysql and python as ewplained in
> Basic BioSQL with Biopoython

OK, mysql vs. postgresql issues.

> I have donwloaded the latest version of both, and tried the example with
> cor6_6.gb
> 
> then I got numerous problems
> 
> I fixed the first one by changing line 104 in cursors from
>             if args is None:
> to :
>             if args is None or args=='':
> 

Where's this line? "args is None" looks like something done to allow the 
empty string; the usual way (to mean what you're using) would be "if not 
args:"

> then in Loader, in def _load_reference(self, reference, rank, bioentry_id):,
> i made the following changes (in particular replaced JOIN by INNER JOIN)
> if reference.medline_id:
>             sql="SELECT reference_id" \
>                 "  FROM reference INNER JOIN dbxref ON reference .dbxref_id
> = dbxref.dbxref_id" \
>                 " WHERE ((dbname = 'MEDLINE') AND (accession = %s))"
>             refs =
> self.adaptor.execute_and_fetch_col0(sql,reference.medline_id)
> 

JOIN -> INNER JOIN: ok
using (field) -> on t1.field = t2.field: *sigh* ok
But are the extraneous parentheses really needed?

> 
> Now, I have one more pb:
> 
> Traceback (most recent call last):
>   File "C:\Python23\RC_databases\rc_BioSQL_GenBank.py", line 21,
> in -toplevel-
>     db.load(iterator)
>   File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 343,
> in load
>     db_loader.load_seqrecord(cur_record)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 46, in
> load_seqrecord
>     self._load_seqfeature(seq_feature, seq_feature_num, bioentry_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 366, in
> _load_seqfeature
>     self._load_seqfeature_locations(feature, seqfeature_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 409, in
> _load_seqfeature_locations
>     self._insert_seqfeature_location(feature, 1, seqfeature_id)
>   File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 430, in
> _insert_seqfeature_location
>     self.adaptor.execute(sql, (seqfeature_id, start, end, strand, rank))
>   File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line 223,
> in execute
>     self.cursor.execute(sql, args)
>   File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 95, in
> execute
>     return self._execute(query, args)
>   File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 119, in
> _execute
>     self.errorhandler(self, exc, value)
>   File "C:\Python23\Lib\site-packages\MySQLdb\connections.py", line 33, in
> defaulterrorhandler
>     raise errorclass, errorvalue
> OperationalError: (1048, "Le champ 'strand' ne peut \xeatre vide (null)")


Hilmar: seems like there's a buglet in biosqldb-pg.sql: strand is 
missing the NOT NULL.

Richard:
Loader.py, line 424
-         strand = feature.strand
+         strand = feature.strand or 0
should do the trick

> 
> 
> I am for the time being only trying some quick and dirty (like modification
> of cursor instead of loader I guess...) changes  to try to get it working
> My questions are :
> Is there somebody else having trouble, or do you I miss something ?
> If I did it right, Is there somebody else trying to fix these problems ?

It seems like you're the first trying these things with MySQL since they 
were last changed. Thanks for the report!

> If things need some help, it would be very nice to have some clear
> description of biosql structure. I have not been able to find it. Somebody
> could help ?
> 
> thanks in advance

De rien,

> 
> Richard CHRISTEN
> Champion de saut en largeur
> UMR6543 CNRS - Universit? de Nice Sophia Antipolis
> 
> Centre de Biochimie
> Parc Valrose
> 06108 Nice cedex2
> 
> tel  33 - 492 076 947
> fax 33 - 492 076 408
> 

yves

From jvhan at pandora.be  Tue Dec  9 15:32:26 2003
From: jvhan at pandora.be (jack van handenhove)
Date: Tue Dec  9 22:16:06 2003
Subject: [BioSQL-l] biosql on sybase?
Message-ID: <003001c3be93$91bdc970$18dca451@acshome>

Dear All,

I am currently investigating the use of bioperl and underlying biosql database to build a repository of genetic data.

as the inhouse database system is sybase, the biosql-db modules should be adapted for use with this system.

could you give an estimation of the amount of work that would be involved in porting these modules to sybase? And what exactly should be done. Which scripts should be adapted? is there only Perl scripts involved or also C?

besides that, the schema should also be migrated, although I do not see a lot of difficulties there. As the schema is stable, it seems like choosing the correct datatypes that correspond to those used in the existing schema. Unless the Oracle schema, which would serve as the model, implements a lot of triggers an stored procedures?

Please know that I am a programmer with moderate perl experience.

Are there other modules besides bioperl-db, that should be ported?

thanks for your reply,
Jack
From raphael.bauer at informatik.hu-berlin.de  Mon Dec 15 10:00:19 2003
From: raphael.bauer at informatik.hu-berlin.de (Raphael A. Bauer)
Date: Mon Dec 15 10:06:11 2003
Subject: [BioSQL-l] One Datasource => One Comment?
Message-ID: <3FDDCC83.9090809@informatik.hu-berlin.de>

Hello BioSQL List,

When I parse Swissprot or Genbank or EMBL into a newly generated biosql 
schema - is it possible that there can be generated more than one 
comment entries for a single bioentry?
I would think that more comments for a single bioentry can only happen 
if there is more than one datasource in the biosql-schema (eg. Genbank 
and Swissprot together).
Am I right?

Thank you very much,

Raphael Bauer

From Marc.Logghe at devgen.com  Mon Dec 15 10:19:12 2003
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Mon Dec 15 10:25:20 2003
Subject: [BioSQL-l] One Datasource => One Comment?
Message-ID: <BEE28BF86078B6429D6C780635718E210395B6@morelia.be.devgen.com>



> -----Original Message-----
> From: Raphael A. Bauer [mailto:raphael.bauer@informatik.hu-berlin.de]
> Sent: Monday, December 15, 2003 4:00 PM
> To: biosql-l@open-bio.org
> Subject: [BioSQL-l] One Datasource => One Comment?
> 
> 
> Hello BioSQL List,
> 
> When I parse Swissprot or Genbank or EMBL into a newly 
> generated biosql 
> schema - is it possible that there can be generated more than one 
> comment entries for a single bioentry?

Sure, that is possible. They even get an internal ranking so that when you fetch the bioentry from biosql and dump it as say, genbank, they end up in the same order as originally entered.

> I would think that more comments for a single bioentry can 
> only happen 
> if there is more than one datasource in the biosql-schema 
> (eg. Genbank 
> and Swissprot together).
> Am I right?
I don't follow you here. Every COMMENT field from the original genbank record becomes a separate entry in the comment table, which is linked to the bioentry via its FK (Bioentry ID)
HTH,
Marc

From hlapp at gnf.org  Mon Dec 15 12:11:12 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Mon Dec 15 12:17:14 2003
Subject: [BioSQL-l] One Datasource => One Comment?
In-Reply-To: <3FDDCC83.9090809@informatik.hu-berlin.de>
Message-ID: <AEDA1528-2F21-11D8-B1CB-000A959EB4C4@gnf.org>


On Monday, December 15, 2003, at 07:00  AM, Raphael A. Bauer wrote:

> Hello BioSQL List,
>
> When I parse Swissprot or Genbank or EMBL into a newly generated 
> biosql schema - is it possible that there can be generated more than 
> one comment entries for a single bioentry?

If the original entry had more than one comment then yes. Swissprot 
should have always only one comment I'd claim, but I really don't know 
for sure.

> I would think that more comments for a single bioentry can only happen 
> if there is more than one datasource in the biosql-schema (eg. Genbank 
> and Swissprot together).
>

This is hardly possible. Theoretically it can happen if you assigned 
the same namespace to both datasources and chose to update records when 
loading the second datasource, but then the records needed to have the 
same accession numbers, which GenBank and Swissprot really don't. 
Otherwise, if you assigned different namespaces the bioentries will be 
different.

	-hilmar

> Am I right?
>
> Thank you very much,
>
> Raphael Bauer
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l@open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From jjliu at cs.nchu.edu.tw  Wed Dec 17 10:15:24 2003
From: jjliu at cs.nchu.edu.tw (Jim Liu)
Date: Wed Dec 17 10:23:36 2003
Subject: [BioSQL-l] Can I just consider import HGI.101403 to biosequence
	table?
References: <AEDA1528-2F21-11D8-B1CB-000A959EB4C4@gnf.org>
Message-ID: <003101c3c4b0$99616150$ee213e3d@jimhome>

Dear All,

I went to ftp://ftp.tigr.org/pub/data/tgi/Homo_sapiens/
and downloaded HGI.release_13.zip.
There are 4 data files:

479,047,691 HGI.101403
  57,653,798 HGI.TC_EST.101403
  12,629,591 HGI.TCs.101403
  10,303,001 HGI.GO.101403

I would like to import to MySQL database.
I already applied BioSQL schema on MySQL.
Can I just consider import HGI.101403 to biosequence table?
How about the other data files?
How to find the detail definition of these data files?

Thanks.

Jim Liu

From hlapp at gnf.org  Wed Dec 17 11:23:26 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Dec 17 11:29:18 2003
Subject: [BioSQL-l] Can I just consider import HGI.101403 to biosequence
	table?
In-Reply-To: <003101c3c4b0$99616150$ee213e3d@jimhome>
Message-ID: <57BCBD9E-30AD-11D8-BADE-000A959EB4C4@gnf.org>


On Wednesday, December 17, 2003, at 07:15  AM, Jim Liu wrote:

> Dear All,
>
> I went to ftp://ftp.tigr.org/pub/data/tgi/Homo_sapiens/
> and downloaded HGI.release_13.zip.
> There are 4 data files:
>
> 479,047,691 HGI.101403
>   57,653,798 HGI.TC_EST.101403
>   12,629,591 HGI.TCs.101403
>   10,303,001 HGI.GO.101403
>
> I would like to import to MySQL database.
> I already applied BioSQL schema on MySQL.
> Can I just consider import HGI.101403 to biosequence table?

You'd also want to populate other tables. Generally I'd think you 
should be able to import those data into biosql; whether or not you can 
use the supplied tools to do it basically depends on whether there is a 
bioperl SeqIO parser for the format. So, check whether the 
SeqIO/tigr.pm XML parser is the one you need here; otherwise you could 
still write your own.

	-hilmar

> How about the other data files?
> How to find the detail definition of these data files?
>
> Thanks.
>
> Jim Liu
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l@open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From laurichj at bioinfo.ucr.edu  Wed Dec 17 12:26:35 2003
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Wed Dec 17 12:32:25 2003
Subject: [BioSQL-l] Can I just consider import HGI.101403 to biosequence
	table?
In-Reply-To: <57BCBD9E-30AD-11D8-BADE-000A959EB4C4@gnf.org>
References: <003101c3c4b0$99616150$ee213e3d@jimhome>
	<57BCBD9E-30AD-11D8-BADE-000A959EB4C4@gnf.org>
Message-ID: <20031217172635.GA16189@bioinfo.ucr.edu>

On Wed 12/17/03 08:23, Hilmar Lapp wrote:
> 
> On Wednesday, December 17, 2003, at 07:15  AM, Jim Liu wrote:
> 
> >Dear All,
> >
> >I went to ftp://ftp.tigr.org/pub/data/tgi/Homo_sapiens/
> >and downloaded HGI.release_13.zip.
> >There are 4 data files:
> >
> >479,047,691 HGI.101403
> >  57,653,798 HGI.TC_EST.101403
> >  12,629,591 HGI.TCs.101403
> >  10,303,001 HGI.GO.101403
> >
> >I would like to import to MySQL database.
> >I already applied BioSQL schema on MySQL.
> >Can I just consider import HGI.101403 to biosequence table?
> 
> You'd also want to populate other tables. Generally I'd think you 
> should be able to import those data into biosql; whether or not you can 
> use the supplied tools to do it basically depends on whether there is a 
> bioperl SeqIO parser for the format. So, check whether the 
> SeqIO/tigr.pm XML parser is the one you need here; otherwise you could 
> still write your own.
> 

Wanting to test SeqIO/tigr.pm on more files I took a look at them...

These files are in various formats, some appear to be search results.
Those can't be imported into BioSQL, as far as I know. The only file
that could be is HGI.101403, which is in Fasta. So the best bet for this
is just to use an index such as Bio::Index::Fasta, unless you want to do
searching on the descriptions. Even then, it wouldn't be to hard to
write a quick and dirty DB_File index for those.

On a side note, is there anything thats more efficient at getting a
sequence from BioSQL than Bio::DB::BioDB? All the transformations done
by that interface make it too slow to use on a webpage.

> >How about the other data files?
> >How to find the detail definition of these data files?
> >
> >Thanks.
> >
> >Jim Liu
> >
> >_______________________________________________
> >BioSQL-l mailing list
> >BioSQL-l@open-bio.org
> >http://open-bio.org/mailman/listinfo/biosql-l
> >
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l@open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
> 

-- 

----------------------------
| Josh Lauricha            |
| laurichj@bioinfo.ucr.edu |
| Bioinformatics, UCR      |
|--------------------------|
From hlapp at gnf.org  Wed Dec 17 13:01:21 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Dec 17 13:07:13 2003
Subject: [BioSQL-l] Can I just consider import HGI.101403 to biosequence
	table?
In-Reply-To: <20031217172635.GA16189@bioinfo.ucr.edu>
Message-ID: <0560C257-30BB-11D8-9AA1-000A959EB4C4@gnf.org>


On Wednesday, December 17, 2003, at 09:26  AM, Josh Lauricha wrote:

> On a side note, is there anything thats more efficient at getting a
> sequence from BioSQL than Bio::DB::BioDB? All the transformations done
> by that interface make it too slow to use on a webpage.
>

Not for perl AFAIK. What is the response time that you're looking for? 
What is the search that you execute?

A single sequence record located by unique key should return in a 
fraction of a second that's shorter than the browser page build-up 
combined with the network latency, provided you back it with a decent 
database server.

Note that the bioperl-db code makes extensive use of caching. If you 
fire up a CGI each and every time you hit the page, you won't take any 
advantage of that.

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


From hlapp at gnf.org  Wed Dec 17 14:07:56 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Dec 17 14:13:47 2003
Subject: [BioSQL-l] Can I just consider import HGI.101403 to biosequence
	table?
In-Reply-To: <20031217185059.GD16189@bioinfo.ucr.edu>
Message-ID: <52C4B319-30C4-11D8-9AA1-000A959EB4C4@gnf.org>


On Wednesday, December 17, 2003, at 10:50  AM, Josh Lauricha wrote:

> The select took basically no time, but the time spent inside Bio::* was
> significant. This is on quad xeon 1.9GHz with 8GB RAM... so it was
> probably something with the local setup, or I'm confusing things.
>

Hm. Try to execute the search with a unique key query 
($adp->find_by_unique_key()). There should be no difference. If there 
is then it hints at a bioperl-db problem, or at a missing or wrong 
index on accession number.

But you say the select was fast. Note that by the time you get the 
record returned as an object, several tens of selects will have been 
executed to fetch all the related entities. The only time this would 
take several seconds is if your accession is for a unigene cluster with 
hundreds or even thousands of members, because each member is a 
bioentry itself.

Note that you can turn on a lot (!) of debugging output by setting 
$db->verbose(1) before you obtain any adaptor or persistent object from 
it. If you then watch the log online, you may see if there's any 
problem query where it stalls briefly. Some people have reported that 
the species retrieval in I believe mysql was a serious bottleneck (and 
then it is the sql query itself). Species are cached once they've been 
retrieved once, but if you restart the script every time you won't take 
advantage of this.

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


From Frederic.Pecqueur at devgen.com  Mon Dec 22 10:05:17 2003
From: Frederic.Pecqueur at devgen.com (Frederic Pecqueur)
Date: Mon Dec 22 10:12:57 2003
Subject: [BioSQL-l] Query Problem.
Message-ID: <BEE28BF86078B6429D6C780635718E21419F8E@morelia.be.devgen.com>

Hi,

I try to create a query to search all the entries which have a tag "other_name" equal to 'mig-11'....and it dosen't work...

I use this code :

my $adp = $db->get_object_adaptor('Bio::PrimarySeqI');

my $query = Bio::DB::Query::BioQuery->new(
                -datacollections => [
                    "Bio::PrimarySeqI entr",
                    "Bio::SeqFeatureI  feat",
                    "Bio::Ontology::TermI  ter",
                    "BioNamespace=>Bio::PrimarySeqI db",
                    "Bio::PrimarySeqI=>Bio::SeqFeatureI",
                    "Bio::SeqFeatureI<=>Bio::Ontology::TermI  qual"
                ],
                -where => ["db.namespace = 'WormGene'",
                           "ter.name = 'other_name'",
                           "qual.value = 'mig-11'"]
);

my $result = $adp->find_by_query($query);

I have this error :

attempting to load driver for adaptor class Bio::DB::BioSQL::PrimarySeqAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as driver peer for Bio::DB::BioSQL::PrimarySeqAdaptor

------------- EXCEPTION  -------------
MSG: Alias "q" not mapped to entity. Are you sure there's no typo?
STACK Bio::DB::Query::BioQuery::_map_slot_to_col /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:466
STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:369
STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:355
STACK Bio::DB::Query::BioQuery::translate_query /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:305
STACK Bio::DB::BioSQL::BaseDriver::translate_query /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BaseDriver.pm:1184
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_query /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1198

I don't use the API correctly?? 
Somebody has a response?

Thanks a lot!
Fr?d?ric.

From hlapp at gnf.org  Mon Dec 22 11:26:32 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Mon Dec 22 11:34:11 2003
Subject: [BioSQL-l] Query Problem.
In-Reply-To: <BEE28BF86078B6429D6C780635718E21419F8E@morelia.be.devgen.com>
Message-ID: <9A94C2C2-349B-11D8-AE25-000A959EB4C4@gnf.org>

This error is pretty weird. Smells like a bug, I'm just not sure where.  
Try collapsing the multiple spaces between entity and alias into a  
single space for every datacollection and see whether it goes away. I  
can't tell where it would get the 'q' as an alias from.

A tip aside from that: I'd request the adaptor for Bio::SeqI or  
otherwise you won't get features and annotation on the resulting  
objects.

	-hilmar

On Monday, December 22, 2003, at 07:05  AM, Frederic Pecqueur wrote:

> Hi,
>
> I try to create a query to search all the entries which have a tag  
> "other_name" equal to 'mig-11'....and it dosen't work...
>
> I use this code :
>
> my $adp = $db->get_object_adaptor('Bio::PrimarySeqI');
>
> my $query = Bio::DB::Query::BioQuery->new(
>                 -datacollections => [
>                     "Bio::PrimarySeqI entr",
>                     "Bio::SeqFeatureI  feat",
>                     "Bio::Ontology::TermI  ter",
>                     "BioNamespace=>Bio::PrimarySeqI db",
>                     "Bio::PrimarySeqI=>Bio::SeqFeatureI",
>                     "Bio::SeqFeatureI<=>Bio::Ontology::TermI  qual"
>                 ],
>                 -where => ["db.namespace = 'WormGene'",
>                            "ter.name = 'other_name'",
>                            "qual.value = 'mig-11'"]
> );
>
> my $result = $adp->find_by_query($query);
>
> I have this error :
>
> attempting to load driver for adaptor class  
> Bio::DB::BioSQL::PrimarySeqAdaptor
> attempting to load driver for adaptor class  
> Bio::DB::BioSQL::BasePersistenceAdaptor
> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as driver  
> peer for Bio::DB::BioSQL::PrimarySeqAdaptor
>
> ------------- EXCEPTION  -------------
> MSG: Alias "q" not mapped to entity. Are you sure there's no typo?
> STACK Bio::DB::Query::BioQuery::_map_slot_to_col  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:466
> STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:369
> STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:355
> STACK Bio::DB::Query::BioQuery::translate_query  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:305
> STACK Bio::DB::BioSQL::BaseDriver::translate_query  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BaseDriver.pm:1184
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_query  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:1198
>
> I don't use the API correctly??
> Somebody has a response?
>
> Thanks a lot!
> Fr?d?ric.
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l@open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



From laurichj at bioinfo.ucr.edu  Tue Dec 23 19:34:17 2003
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Tue Dec 23 19:41:44 2003
Subject: [BioSQL-l] Can I just consider import HGI.101403 to biosequence
	table?
In-Reply-To: <52C4B319-30C4-11D8-9AA1-000A959EB4C4@gnf.org>
References: <20031217185059.GD16189@bioinfo.ucr.edu>
	<52C4B319-30C4-11D8-9AA1-000A959EB4C4@gnf.org>
Message-ID: <20031224003417.GB15277@bioinfo.ucr.edu>

On Wed 12/17/03 11:07, Hilmar Lapp wrote:
> Hm. Try to execute the search with a unique key query 
> ($adp->find_by_unique_key()). There should be no difference. If there 
> is then it hints at a bioperl-db problem, or at a missing or wrong 
> index on accession number.

The code that I can still find from playing with this ran fine, so it
must have been something I was doing. Unfortunatly, I don't have that
code anymore.

-- 

----------------------------
| Josh Lauricha            |
| laurichj@bioinfo.ucr.edu |
| Bioinformatics, UCR      |
|--------------------------|
From Richard.Holland at agresearch.co.nz  Mon Dec 29 22:07:51 2003
From: Richard.Holland at agresearch.co.nz (Holland, Richard)
Date: Tue Dec 30 12:39:35 2003
Subject: [BioSQL-l] Cannot make test on bioperl-db
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165013375F9@inbox.agresearch.co.nz>

Apologies for the cross-post but I am not sure if it is BioSQL or
BioPerl at fault here.

I have installed the Oracle version of BioSQL and bioperl-db as
downloaded last week, and they compile and install fine. However, make
test on bioperl-db fails miserably with hundreds of messages similar to
the following on virtually every module:

---SNIP---
bifo6.agresearch.co.nz> make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/cluster.......ok 155/160DBD::Oracle::st execute failed: ORA-00001:
unique constraint (SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD
ERROR: OCIStmtExecute) [for Statement "INSERT INTO
bioentry_qualifier_value (ent_oid, trm_oid, value, rank) VALUES (?, ?,
?, ?)" with ParamValues: :p3='ORG=Escherischia coli; PROTGI=8928262;
PROTID=Ec_pid; PCT=24; ALN=254', :p1='417', :p4=1, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD ERROR:
OCIStmtExecute) [for Statement "INSERT INTO bioentry_qualifier_value
(ent_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)" with ParamValues:
:p3='ORG=Homo sapiens; PROTGI=114238; PROTID=sp:P11245; PCT=100;
ALN=289', :p1='417', :p4=2, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD ERROR:
OCIStmtExecute) [for Statement "INSERT INTO bioentry_qualifier_value
(ent_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)" with ParamValues:
:p3='ORG=Mus musculus; PROTGI=1703436; PROTID=sp:P50295; PCT=74;
ALN=289', :p1='417', :p4=3, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD ERROR:
OCIStmtExecute) [for Statement "INSERT INTO bioentry_qualifier_value
(ent_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)" with ParamValues:
:p3='ORG=Rattus norvegicus; PROTGI=1703437; PROTID=sp:P50298; PCT=73;
ALN=289', :p1='417', :p4=4, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
---SNIP---

My installation includes the text indexer option, and I have run the
script to load the taxon information (which incidentally took almost 20
hours to run on a three-processor Compaq Alpha with 11 gigs of RAM -
that's also a bit of a worry, surely?).

The only tables with any data in (I have checked this) are taxon and
taxon_name. The test failed before I loaded the taxon information in
exactly the same way as it does now.

I am wary of wasting time trying to load real data if the test fails
like this - is it a 'fatal' problem or can I ignore it and load real
data anyway?

Any idea what's going on here? I can't figure it out.

cheers,
Richard

---
Richard Holland
Bioinformatics Database Developer
ITS, Agresearch Invermay x3279



=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================