Problems with displaying details page on CHADO

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Problems with displaying details page on CHADO

Michael Dondrup
I have set up Gbrowse2 on a Chado backend and sequences and gff3 annotations. The primary display of the data is working fine,
however I have problems with viewing the details page. I used the following urls to test details pages but to no avail:
http://localhost:8888/cgi-bin/gb2/gbrowse_details/lsalmonis/?name=clc1305s1.1
The primary symptom is that the script is just timed out. This also works fine with the yeast examples.

I have tried different features and made sure they are contained in the database, e.g. supercontigs and exons, further the
search for these features works when the browser page search (e.g. http://localhost:8888/cgi-bin/gb2/gbrowse/lsalmonis/?name=clc1305s1.1).

Other symptoms:
 - The only useful log output from the server:
[Mon Mar 19 14:53:45 2012] [error] [client 127.0.0.1] Use of uninitialized value $base_start in subtraction (-) at /opt/local/lib/perl5/site_perl/5.12.3/Bio/DB/Das/Chado/Segment.pm line 967.

- While doing the search many SQL-queries like the following are performed:

SELECT COALESCE(f.name,f.uniquename) AS seq_id FROM feature f join featureloc fl ON (f.feature_id = fl.srcfeature_id) WHERE fl.feature_id = 345709 AND fl.rank = 0
(tried some and the result is always the name of a (different) supercontig e.g. clc1305s1.1)

I have the impression that  way too many queries are issued for a single entry.

Versions:
GBrowse 2.48
Bio::DB::Das::Chado 0.33
Postgres 9.1.2
Perl This is perl 5, version 12, subversion 3 (v5.12.3) built for darwin-thread-multi-2level

Thanks so much for any hints.



Michael Dondrup
Post-doctoral researcher
The Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway


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Re: [Gmod-gbrowse] Problems with displaying details page on CHADO

Scott Cain
Hi Michael,

It can be really hard to debug this sort of thing remotely; it is
almost always due to something in the GFF that that adaptor isn't
expecting (I don't want to call it something "wrong" as it may not
technically be wrong, just unexpected :-)  If you could send me a
sample of the GFF that resulted in the bad behavior I can probably
tell you what is going on.

Scott


On Mon, Mar 19, 2012 at 10:36 AM, Michael Dondrup
<[hidden email]> wrote:

> I have set up Gbrowse2 on a Chado backend and sequences and gff3 annotations. The primary display of the data is working fine,
> however I have problems with viewing the details page. I used the following urls to test details pages but to no avail:
> http://localhost:8888/cgi-bin/gb2/gbrowse_details/lsalmonis/?name=clc1305s1.1
> The primary symptom is that the script is just timed out. This also works fine with the yeast examples.
>
> I have tried different features and made sure they are contained in the database, e.g. supercontigs and exons, further the
> search for these features works when the browser page search (e.g. http://localhost:8888/cgi-bin/gb2/gbrowse/lsalmonis/?name=clc1305s1.1).
>
> Other symptoms:
>  - The only useful log output from the server:
> [Mon Mar 19 14:53:45 2012] [error] [client 127.0.0.1] Use of uninitialized value $base_start in subtraction (-) at /opt/local/lib/perl5/site_perl/5.12.3/Bio/DB/Das/Chado/Segment.pm line 967.
>
> - While doing the search many SQL-queries like the following are performed:
>
> SELECT COALESCE(f.name,f.uniquename) AS seq_id FROM feature f join featureloc fl ON (f.feature_id = fl.srcfeature_id) WHERE fl.feature_id = 345709 AND fl.rank = 0
> (tried some and the result is always the name of a (different) supercontig e.g. clc1305s1.1)
>
> I have the impression that  way too many queries are issued for a single entry.
>
> Versions:
> GBrowse 2.48
> Bio::DB::Das::Chado 0.33
> Postgres 9.1.2
> Perl This is perl 5, version 12, subversion 3 (v5.12.3) built for darwin-thread-multi-2level
>
> Thanks so much for any hints.
>
>
>
> Michael Dondrup
> Post-doctoral researcher
> The Sea Lice Research Centre
> Department of Informatics
> University of Bergen
> Thormøhlensgate 55, N-5008 Bergen,
> Norway
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: [Gmod-gbrowse] Problems with displaying details page on CHADO

Michael Dondrup
Hi Scott,

I have sort of solved it by using feature_id instead of name in the  
query like so in the config file:
link =  
/cgi-bin/gb2/gbrowse_details/lsalmonis/feature_id=$id;db_id=annotations%3Adatabase
instead of only providing the name. I am not sure if further debugging  
is warranted, maybe just in case it is supposed to work with name only  
(which I copied from the yeast example configuration). I should also  
say that I had
the following configuration for the databases, while  I had not  
prepared the database for fulltext search (as required in the  
documentation for chado):

[scaffolds:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn  'dbi:Pg:dbname=lsalmonis_chado;host=localhost'
                 -user 'mdondrup'
                 -pass xxx
                 -srcfeatureslice 1
search options = all

[annotations:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn  'dbi:Pg:dbname=lsalmonis_chado;host=localhost'
                 -user 'mdondrup'
                 -pass  xxx
                 -srcfeatureslice 1
search options = all

Unfortunately I may not give you the full data for testing, but the  
onlyfeature that is special about them is that is contains very many  
supercontigs > 20k at the moment.

Thank you very much
Michael


Quoting Scott Cain <[hidden email]>:

> Hi Michael,
>
> It can be really hard to debug this sort of thing remotely; it is
> almost always due to something in the GFF that that adaptor isn't
> expecting (I don't want to call it something "wrong" as it may not
> technically be wrong, just unexpected :-)  If you could send me a
> sample of the GFF that resulted in the bad behavior I can probably
> tell you what is going on.
>
> Scott
>
>
> On Mon, Mar 19, 2012 at 10:36 AM, Michael Dondrup
> <[hidden email]> wrote:
>> I have set up Gbrowse2 on a Chado backend and sequences and gff3  
>> annotations. The primary display of the data is working fine,
>> however I have problems with viewing the details page. I used the  
>> following urls to test details pages but to no avail:
>> http://localhost:8888/cgi-bin/gb2/gbrowse_details/lsalmonis/?name=clc1305s1.1
>> The primary symptom is that the script is just timed out. This also  
>> works fine with the yeast examples.
>>
>> I have tried different features and made sure they are contained in  
>> the database, e.g. supercontigs and exons, further the
>> search for these features works when the browser page search (e.g.  
>> http://localhost:8888/cgi-bin/gb2/gbrowse/lsalmonis/?name=clc1305s1.1).
>>
>> Other symptoms:
>>  - The only useful log output from the server:
>> [Mon Mar 19 14:53:45 2012] [error] [client 127.0.0.1] Use of  
>> uninitialized value $base_start in subtraction (-) at  
>> /opt/local/lib/perl5/site_perl/5.12.3/Bio/DB/Das/Chado/Segment.pm  
>> line 967.
>>
>> - While doing the search many SQL-queries like the following are performed:
>>
>> SELECT COALESCE(f.name,f.uniquename) AS seq_id FROM feature f join  
>> featureloc fl ON (f.feature_id = fl.srcfeature_id) WHERE  
>> fl.feature_id = 345709 AND fl.rank = 0
>> (tried some and the result is always the name of a (different)  
>> supercontig e.g. clc1305s1.1)
>>
>> I have the impression that  way too many queries are issued for a  
>> single entry.
>>
>> Versions:
>> GBrowse 2.48
>> Bio::DB::Das::Chado 0.33
>> Postgres 9.1.2
>> Perl This is perl 5, version 12, subversion 3 (v5.12.3) built for  
>> darwin-thread-multi-2level
>>
>> Thanks so much for any hints.
>>
>>
>>
>> Michael Dondrup
>> Post-doctoral researcher
>> The Sea Lice Research Centre
>> Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>>
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

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Re: [Gmod-gbrowse] Problems with displaying details page on CHADO

Scott Cain
Hi Michael,

When you were using gbrowse_details before and it wasn't working, it
was just linking from gbrowse, not from somewhere else, right?  I
thought I had that working correctly even when there are ambiguous
names, but perhaps I haven't worked out some edge case.  Certainly,
your work around is a good one, as feature_id should always work with
gbrowse_details and Chado.

Scott


On Fri, Mar 23, 2012 at 10:21 AM,  <[hidden email]> wrote:

> Hi Scott,
>
> I have sort of solved it by using feature_id instead of name in the query
> like so in the config file:
> link =
> /cgi-bin/gb2/gbrowse_details/lsalmonis/feature_id=$id;db_id=annotations%3Adatabase
> instead of only providing the name. I am not sure if further debugging is
> warranted, maybe just in case it is supposed to work with name only (which I
> copied from the yeast example configuration). I should also say that I had
> the following configuration for the databases, while  I had not prepared the
> database for fulltext search (as required in the documentation for chado):
>
> [scaffolds:database]
> db_adaptor    = Bio::DB::Das::Chado
> db_args       = -dsn  'dbi:Pg:dbname=lsalmonis_chado;host=localhost'
>                -user 'mdondrup'
>                -pass xxx
>                -srcfeatureslice 1
> search options = all
>
> [annotations:database]
> db_adaptor    = Bio::DB::Das::Chado
> db_args       = -dsn  'dbi:Pg:dbname=lsalmonis_chado;host=localhost'
>                -user 'mdondrup'
>                -pass  xxx
>                -srcfeatureslice 1
> search options = all
>
> Unfortunately I may not give you the full data for testing, but the
> onlyfeature that is special about them is that is contains very many
> supercontigs > 20k at the moment.
>
> Thank you very much
> Michael
>
>
>
> Quoting Scott Cain <[hidden email]>:
>
>> Hi Michael,
>>
>> It can be really hard to debug this sort of thing remotely; it is
>> almost always due to something in the GFF that that adaptor isn't
>> expecting (I don't want to call it something "wrong" as it may not
>> technically be wrong, just unexpected :-)  If you could send me a
>> sample of the GFF that resulted in the bad behavior I can probably
>> tell you what is going on.
>>
>> Scott
>>
>>
>> On Mon, Mar 19, 2012 at 10:36 AM, Michael Dondrup
>> <[hidden email]> wrote:
>>>
>>> I have set up Gbrowse2 on a Chado backend and sequences and gff3
>>> annotations. The primary display of the data is working fine,
>>> however I have problems with viewing the details page. I used the
>>> following urls to test details pages but to no avail:
>>>
>>> http://localhost:8888/cgi-bin/gb2/gbrowse_details/lsalmonis/?name=clc1305s1.1
>>> The primary symptom is that the script is just timed out. This also works
>>> fine with the yeast examples.
>>>
>>> I have tried different features and made sure they are contained in the
>>> database, e.g. supercontigs and exons, further the
>>> search for these features works when the browser page search (e.g.
>>> http://localhost:8888/cgi-bin/gb2/gbrowse/lsalmonis/?name=clc1305s1.1).
>>>
>>> Other symptoms:
>>>  - The only useful log output from the server:
>>> [Mon Mar 19 14:53:45 2012] [error] [client 127.0.0.1] Use of
>>> uninitialized value $base_start in subtraction (-) at
>>> /opt/local/lib/perl5/site_perl/5.12.3/Bio/DB/Das/Chado/Segment.pm line 967.
>>>
>>> - While doing the search many SQL-queries like the following are
>>> performed:
>>>
>>> SELECT COALESCE(f.name,f.uniquename) AS seq_id FROM feature f join
>>> featureloc fl ON (f.feature_id = fl.srcfeature_id) WHERE fl.feature_id =
>>> 345709 AND fl.rank = 0
>>> (tried some and the result is always the name of a (different)
>>> supercontig e.g. clc1305s1.1)
>>>
>>> I have the impression that  way too many queries are issued for a single
>>> entry.
>>>
>>> Versions:
>>> GBrowse 2.48
>>> Bio::DB::Das::Chado 0.33
>>> Postgres 9.1.2
>>> Perl This is perl 5, version 12, subversion 3 (v5.12.3) built for
>>> darwin-thread-multi-2level
>>>
>>> Thanks so much for any hints.
>>>
>>>
>>>
>>> Michael Dondrup
>>> Post-doctoral researcher
>>> The Sea Lice Research Centre
>>> Department of Informatics
>>> University of Bergen
>>> Thormøhlensgate 55, N-5008 Bergen,
>>> Norway
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF email is sponsosred by:
>>> Try Windows Azure free for 90 days Click Here
>>> http://p.sf.net/sfu/sfd2d-msazure
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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