[BioSQL-l] BioSQL-1.0.0 + bioperl-db_1.5.2_100 + gbrowse question
Hilmar Lapp
hlapp at gmx.net
Wed Apr 9 04:31:31 UTC 2008
Hi Doug,
thanks for your sleuthing work, it's much appreciated. I'm sure
someone among the GBrowse crowd (I've copied the GBrowse mailing
list) can make the fix according to what you found out, and they can
help you out with the other problems you are having too if you
elaborate what the issues are that you are seeing.
As for the path tables, which ones are you referring to? I'm not sure
the GBrowse BioSQL adapter uses any of them, so even if you do
populate them it wouldn't change much. There is the load_ontology.pl
script in Bioperl-db that can automatically compute the transitive
closure for ontology terms, but as far as I am aware the feature or
sequence loading scripts don't do that for seqfeature_path or
bioentry_path, respectively.
-hilmar
On Apr 7, 2008, at 4:51 PM, doug brown wrote:
> Hi Hilmar,
>
> Thank you for your reply.
>
> After much gnashing of teeth and much more code trawling, it
> seems as it the basic problem I encountered was indeed one of
> configuration. The current coding of
> Bio::DB::Das::BioSQL::BioDatabaseAdaptor uses 'location' as the
> keyword for representing the database host. The GFF adapter used,
> and I guess still uses, 'host' for that purpose. The distributed
> sample file 06.biosql.conf specified 'host' rather than 'location'.
> Here is the correct configuration file section that now works for me:
>
> description = Magnaporthe grisea V5 genbank BioSQL
> db_args = driver mysql
> dbname M_grisea_genbank_biosql
> location mycelium.fgl.ncsu.edu
> user www
> pass ""
> namespace genbank
> version 1
>
> gbrowse starts up OK now. Could you please tell me whom would be
> the responsible party so that I can send him/her a note? There are
> also other problems with the file that I am trying to resolve.
> Thank you.
>
> Now I need to figure out how to get gbrowse to display all of my
> features (I finally have a database rich enough to represent them
> but not so complex as to be unwieldy) .....
>
> Oh, I noticed that the various path tables are not populated and
> one piece of documentation said something about "... database
> dependent...". Could you point me to any code samples that populate
> those tables? Or, perhaps, pointers to specific mailing list
> message chains even.
>
> In general, any clues or bread crumbs would be greatly appreciated.
>
> Regards,
> Doug Brown
>
> Hilmar Lapp wrote:
>>
>> Hi Doug,
>>
>> I'm not exactly sure what the problem is but the error you are
>> seeing is raised by code with GBrowse. I'd recommend that you post
>> this to the GBrowse list. I have tried to trace the meaning of the
>> Gbrowse conf parameters, and it seems to me that biodbname is
>> obsolete and should be namespace instead. However, I also can't
>> find where the error is being generated using the error message as
>> guide, so I suspect you are using an outdated version of GBrowse.
>> The folks on the Gbrowse list should be able to tell you more
>> specifics, though.
>>
>> -hilmar
>>
>> On Apr 3, 2008, at 3:26 PM, doug brown wrote:
>>> Hello Hilmar,
>>>
>>> First off, congratulations for achieving the version 1.0
>>> release of BioSQL.
>>>
>>> I am attempting to get BioSQL working with bioperl and gbrowse.
>>> All are, I believe, the most recent versions of the software.
>>> Unfortunately, I cam running into problems with getting gbrowse
>>> to access the BioSQL database.
>>>
>>> It is my sincere hope that my problem is a configuration issue.
>>> However, after trying multiple permutations of gbrowse
>>> configuration params and much trawling through the bioperl code,
>>> I am unable to resolve the problem. Could you take a moment and
>>> see if there is an obvious solution to my problem?
>>>
>>> I have long awaited the 1.0 mature release of BioSQL and I am
>>> eager to start using it in place my my ad hoc in-house databases!
>>>
>>> Here is the error from the apache log files:
>>> ------------- EXCEPTION -------------
>>> MSG: error while executing query in
>>> Bio::DB::Das::BioSQL::PartialSeqAdaptor::find_by_query: No
>>> database selected
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_query /
>>> Library/Perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1248
>>> STACK
>>> Bio::DB::Das::BioSQL::BioDatabaseAdaptor::fetch_Seq_by_accession /
>>> Library/Perl/5.8.6/darwin-thread-multi-2level/Bio/DB/Das/BioSQL/
>>> BioDatabaseAdaptor.pm:120
>>> STACK Bio::DB::Das::BioSQL::get_feature_by_name /Library/Perl/
>>> 5.8.6/darwin-thread-multi-2level/Bio/DB/Das/BioSQL.pm:220
>>> STACK Bio::Graphics::Browser::_feature_get /Library/Perl/5.8.6/
>>> darwin-thread-multi-2level/Bio/Graphics/Browser.pm:1884
>>> STACK Bio::Graphics::Browser::name2segments /Library/Perl/5.8.6/
>>> darwin-thread-multi-2level/Bio/Graphics/Browser.pm:1828
>>> STACK main::lookup_features_from_db /Library/WebServer/CGI-
>>> Executables/gbrowse:1677
>>> STACK main::get_features /Library/WebServer/CGI-Executables/
>>> gbrowse:1577
>>> STACK toplevel /Library/WebServer/CGI-Executables/gbrowse:182
>>>
>>> My configuration file:
>>> [GENERAL]
>>> # based on 06.biosql.conf,v 1.2.6.2.2.1 2006/06/07 20:50:29 which
>>> was obtained
>>> # from the basic gbrowse installation
>>> description = Magnaporthe grisea V5 genbank BioSQL
>>> db_adaptor = Bio::DB::Das::BioSQL
>>> #nb: the dashes are required and were missing in the original
>>> db_args = driver mysql
>>> -dbname M_grisea_genbank_biosql
>>> -namespace bioperl
>>> -biodbname genbank
>>> -version 1
>>> -host mycelium.fgl.ncsu.edu
>>> -user www
>>> -pass ""
>>> -port 3306
>>>
>>> plugins = FastaDumper RestrictionAnnotator
>>> # deb 2-apr-08 SequenceDumper can't be found. So, dont use it.
>>> #SequenceDumper
>>>
>>> ... remainder is unchanged ...
>>>
>>> database creation and load:
>>> mysql -udebrown -p -h mycelium.fgl.ncsu.edu
>>> drop database M_grisea_genbank_biosql;
>>> create database M_grisea_genbank_biosql;
>>> grant select on M_grisea_genbank_biosql.* to
>>> www at marray.fgl.ncsu.edu;
>>> use M_grisea_genbank_biosql;
>>>
>>> mysql -udebrown -p -h mycelium.fgl.ncsu.edu
>>> M_grisea_genbank_biosql <C:\installKits\biosql-1.0.0\sql\biosqldb-
>>> mysql.sql
>>>
>>> C:\Perl\site\bin\load_seqdatabase.bat\load_seqdatabase.bat --dsn
>>> "dbi:mysql:database=M_grisea_genbank_biosql;host=mycelium.fgl.ncsu.e
>>> du" -dbuser debrown --dbpass XXXXXXX --format genbank genbank
>>> \CH476760.gb --namespace genbank
>>>
>>> machine (node) layout:
>>> marray.fgl.ncsu.edu is the web server
>>> mycelium.fgl.ncsu.edu is the database server
>>> dougslaptop.fgl.ncsu.edu is a development system.
>>>
>>>
>>> Thank you for your time,
>>>
>>> Regards,
>>> Doug Brown
>>> --
>>> Doug Brown - Bioinformatics
>>> Fungal Genomics Laboratory
>>> Center for Integrated Fungal Research
>>> North Carolina State University
>>> Campus Box 7251, Raleigh, NC 27695-7251
>>> https://www.fungalgenomics.ncsu.edu/~debrown/
>>> Tel: (919) 513-0394, Fax (919) 513-0024
>>> e-mail: doug_brown at ncsu.edu
>>>
>>
>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>
> --
> Doug Brown - Bioinformatics
> Fungal Genomics Laboratory
> Center for Integrated Fungal Research
> North Carolina State University
> Campus Box 7251, Raleigh, NC 27695-7251
> https://www.fungalgenomics.ncsu.edu/~debrown/
> Tel: (919) 513-0394, Fax (919) 513-0024
> e-mail: doug_brown at ncsu.edu
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================
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