gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] Controlled Vocabularies data

[Arnaud K. <ax...@sa...>]

Hi Steve

Steve Fischer wrote:

> Arnaud-
>
> first, about DoTS::GeneInstanceCategory.  we don't seem to be using 
> this table.  its empty in our instance. 

We want to generate gene, RNA and protein entries and link them to 
corresponding gene, RNA and protein feature entries. This is done using 
the Gene, RNA and Protein Instance entries.
There is a FK to a GeneInstanceCategory entry in GeneInstance and this 
can not be null. The same for RNAInstance and for ProteinInstance, I'm 
not sure what they are for.

>
>
> second, about the other vocabs.  there is no central resource 
> available. each is dealt with individually.  for example, sres.taxon 
> has a plugin which loads data from ncbi.  sres.anatomy exists uniquely 
> in our db and was created manually.

I'm thinking of CVs such as Taxon with has its own plugin and that the 
data can be retrieve from NCBI.
There are a few ones, GUS specific, that we could share, e.g. 
SRes::OntologyRelationshipType 
<http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=SRes::OntologyRelationshipType&path=SRes::OntologyRelationshipType> 
(AFAIR two entries "part_of" and "is_a"). They could be stored in XML 
format or as SQL statements. I'm thinking of others CVs, I'll prepare a 
list.

>
> so, to best answer your question we would need to know which CVs you 
> want to populate.
>
> steve
>
> Arnaud Kerhornou wrote:
>
>> Hi
>>
>> We would like to populate some of the GUS Controlled Vocabulary 
>> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of 
>> SRes tables.
>> Are these resources available in XML format or in SQL statements from 
>> gusdb website or from CVS ?
>>
>> cheers and happy thanksgiving !!
>> Arnaud
>>
>>

Re: [Gusdev-gusdev] Controlled Vocabularies data

[Steve F. <sfi...@pc...>]

Arnaud-

first, about DoTS::GeneInstanceCategory.  we don't seem to be using this 
table.  its empty in our instance.

second, about the other vocabs.  there is no central resource available. 
 each is dealt with individually.  for example, sres.taxon has a plugin 
which loads data from ncbi.  sres.anatomy exists uniquely in our db and 
was created manually.

so, to best answer your question we would need to know which CVs you 
want to populate.

steve

Arnaud Kerhornou wrote:

> Hi
>
> We would like to populate some of the GUS Controlled Vocabulary 
> tables. I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of 
> SRes tables.
> Are these resources available in XML format or in SQL statements from 
> gusdb website or from CVS ?
>
> cheers and happy thanksgiving !!
> Arnaud
>
>
>
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[Gusdev-gusdev] Controlled Vocabularies data

[Arnaud K. <ax...@sa...>]

Hi

We would like to populate some of the GUS Controlled Vocabulary tables. 
I'm thinking of DoTS::GeneInstanceCategory, and of a bunch of SRes tables.
Are these resources available in XML format or in SQL statements from 
gusdb website or from CVS ?

cheers and happy thanksgiving !!
Arnaud

Re: [Gusdev-gusdev] Sanger CVS

[Pjm <pj...@sa...>]

Angel,

I got this reply from one of our sys admins;

"The cvs server got overwhelmed by the tarball download option. I'm going
to take a look at the config to see if we can stop that from happening
again."

There are 2 different servers for the read only (cvsro.sanger.ac.uk) and 
read/write (cvs.sanger.ac.uk).

Paul.

Angel Pizarro wrote:
> OK, so I was following the instructions on the webserver's page and they 
> did not work for me (e.g. the timeout for cv...@cv... ) 
> but it did work for the developer's with direct access (e.g. 
> an...@cv... )
> 
> Angel
> 
> On Nov 24, 2003, at 11:30 AM, Steve Fischer wrote:
> 
>> Yes, we should provide a tarball... eventually, but i don't think we 
>> are ready for that overhead right now.   about the timing out, in 
>> general the cvs at sanger is quite responsive, so we should assume 
>> that is a temporary glitch, and if not ask manager to fix it.
>>
>> steve
>>
>> Angel Pizarro wrote:
>>
>>> trying to do a checkout of the GUS project from sanger's CVS and it 
>>> is timing out on me. Any problems over at that end? Should we provide 
>>> a stable tarball, like we do for CBIL utils?
>>> Angel
>>>
>>>
>>>
>>> -------------------------------------------------------
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>>
>>
> 
> 
> 
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Re: [Gusdev-gusdev] Sanger CVS

[Angel P. <an...@pc...>]

OK, so I was following the instructions on the webserver's page and 
they did not work for me (e.g. the timeout for 
cv...@cv... ) but it did work for the developer's with 
direct access (e.g. an...@cv... )

Angel

On Nov 24, 2003, at 11:30 AM, Steve Fischer wrote:

> Yes, we should provide a tarball... eventually, but i don't think we 
> are ready for that overhead right now.   about the timing out, in 
> general the cvs at sanger is quite responsive, so we should assume 
> that is a temporary glitch, and if not ask manager to fix it.
>
> steve
>
> Angel Pizarro wrote:
>
>> trying to do a checkout of the GUS project from sanger's CVS and it 
>> is timing out on me. Any problems over at that end? Should we provide 
>> a stable tarball, like we do for CBIL utils?
>> Angel
>>
>>
>>
>> -------------------------------------------------------
>> This SF.net email is sponsored by: SF.net Giveback Program.
>> Does SourceForge.net help you be more productive?  Does it
>> help you create better code?  SHARE THE LOVE, and help us help
>> YOU!  Click Here: http://sourceforge.net/donate/
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] Sanger CVS

[Steve F. <sfi...@pc...>]

Yes, we should provide a tarball... eventually, but i don't think we are 
ready for that overhead right now.   about the timing out, in general 
the cvs at sanger is quite responsive, so we should assume that is a 
temporary glitch, and if not ask manager to fix it.

steve

Angel Pizarro wrote:

> trying to do a checkout of the GUS project from sanger's CVS and it is 
> timing out on me. Any problems over at that end? Should we provide a 
> stable tarball, like we do for CBIL utils?
> Angel
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive?  Does it
> help you create better code?  SHARE THE LOVE, and help us help
> YOU!  Click Here: http://sourceforge.net/donate/
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] Sanger CVS

[Angel P. <an...@pc...>]

trying to do a checkout of the GUS project from sanger's CVS and it is 
timing out on me. Any problems over at that end? Should we provide a 
stable tarball, like we do for CBIL utils?
Angel

[Gusdev-gusdev] InsertNewExternalSequences errors

[sucheta T. <su...@vb...>]

Hi Steve,

I  used only one table name but, the plugin does not seem to upload any
data to the externalnasequence table that I specify.

I have used the following option:

ga GUS::Common::Plugin::InsertNewExternalSequences --debug
--external_database_release_id=1  --no_check  --sequencefile=/usr
/local/src/gus-related/seq/soybean_clean.seq
--table_name=DoTS::ExternalNASequence --update --sqlVerbose
--writeFile=/usr/lo
cal/src/gus-related/seq/temp >& /home/apps/oracle/externalna_err1 --commit

It runs for a while and comes out without any error messages. The last few
lines of the error file is :

bindValues (123, Run finished: Processed 3721, inserted 28 and updated 
sequences from file /usr/local/src/gus-related/seq
/soybean_clean.seq, 123)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

the 28 records are inserted into some of the core tables.

Thanks

Sucheta




> sucheta-
>
> looking at the plugin code, it seems that you can only specify one table
> to insert into.
>
> but, you are inserting into two:
>
> --table_name=DoTS::ExternalNASequence, DoTS::VirtualSequence
>
> as far as which table to use, what is the data you are inserting?
>
> steve
>
> sucheta Tripathy wrote:
>
>>Hi Steve,
>>
>>I used the GUS::Common::Plugin::InsertNewExternalSequences for uploading
>>our local nucleotide sequences with the following parameters:
>>
>>ga GUS::Common::Plugin::InsertNewExternalSequences --algoinvo=2
>>--comment=Loading external NA Sequence --debug
>>--external_database_release_id=1 --no_check --seq
>>uence_type_id=1
>>--sequencefile=/usr/local/src/gus-related/seq/soybean_clean.seq
>>--startAt=0 --table_name=DoTS::ExternalNASequence, DoTS::VirtualSequence
>>--taxon
>>_id=143371 --update --sqlVerbose
>>--writeFile=/usr/local/src/gus-related/seq/temp
>> >& /home/apps/oracle/externalna_err1
>>
>>It gives me the following error:
>>
>>Can't locate object method "new" via package "_Table" at
>>/home/apps/gus/gushome/
>>lib/perl/GUS/ObjRelP/DbiDatabase.pm line 179.
>>
>>My assumption is that since we are using a view name in the table_name
>>parameter it gives the error. In case that is the problem, can you please
>>tell us which table the data should go without violating much of the
>>dependencies?
>>
>>Thanks in advance
>>
>>Sucheta
>>
>>
>>
>
>
>
> -------------------------------------------------------
> This SF. Net email

[Gusdev-gusdev] Re: InsertNewExternalSequences errors

[Steve F. <sfi...@pc...>]

sucheta-

looking at the plugin code, it seems that you can only specify one table 
to insert into.
 
but, you are inserting into two:

--table_name=DoTS::ExternalNASequence, DoTS::VirtualSequence

as far as which table to use, what is the data you are inserting?

steve

sucheta Tripathy wrote:

>Hi Steve,
>
>I used the GUS::Common::Plugin::InsertNewExternalSequences for uploading
>our local nucleotide sequences with the following parameters:
>
>ga GUS::Common::Plugin::InsertNewExternalSequences --algoinvo=2
>--comment=Loading external NA Sequence --debug
>--external_database_release_id=1 --no_check --seq
>uence_type_id=1
>--sequencefile=/usr/local/src/gus-related/seq/soybean_clean.seq
>--startAt=0 --table_name=DoTS::ExternalNASequence, DoTS::VirtualSequence
>--taxon
>_id=143371 --update --sqlVerbose
>--writeFile=/usr/local/src/gus-related/seq/temp
> >& /home/apps/oracle/externalna_err1
>
>It gives me the following error:
>
>Can't locate object method "new" via package "_Table" at
>/home/apps/gus/gushome/
>lib/perl/GUS/ObjRelP/DbiDatabase.pm line 179.
>
>My assumption is that since we are using a view name in the table_name
>parameter it gives the error. In case that is the problem, can you please
>tell us which table the data should go without violating much of the
>dependencies?
>
>Thanks in advance
>
>Sucheta
>
>  
>

[Gusdev-gusdev] InsertNewExternalSequences errors

[sucheta T. <su...@vb...>]

Hi Steve,

I used the GUS::Common::Plugin::InsertNewExternalSequences for uploading
our local nucleotide sequences with the following parameters:

ga GUS::Common::Plugin::InsertNewExternalSequences --algoinvo=2
--comment=Loading external NA Sequence --debug
--external_database_release_id=1 --no_check --seq
uence_type_id=1
--sequencefile=/usr/local/src/gus-related/seq/soybean_clean.seq
--startAt=0 --table_name=DoTS::ExternalNASequence, DoTS::VirtualSequence
--taxon
_id=143371 --update --sqlVerbose
--writeFile=/usr/local/src/gus-related/seq/temp
 >& /home/apps/oracle/externalna_err1

It gives me the following error:

Can't locate object method "new" via package "_Table" at
/home/apps/gus/gushome/
lib/perl/GUS/ObjRelP/DbiDatabase.pm line 179.

My assumption is that since we are using a view name in the table_name
parameter it gives the error. In case that is the problem, can you please
tell us which table the data should go without violating much of the
dependencies?

Thanks in advance

Sucheta

-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138

Re: [Gusdev-gusdev] about uploading RAD data problem

[sam w. <gus...@ya...>]

Dear Elisabetta,
 
thank you very much for your great help! now I am trying according to your suggestion, besides, it seems a little complicated :-)
 
Thanks again,
Sammy

Elisabetta Manduchi <man...@pc...> wrote:

Dear Sam,
regarding the part of your question referring to the manufacturer_id 
error, if you look at schemaBrowser for RAD3.Array at 
http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=RAD3::Array&path=RAD3::Array
you should see that manufacturer_id and platform_type_id are nonnullable. 
Thus a valid manufacturer_id and a valid platform_type_id must be given 
when running the ArrayLoader plugin (see also plugin documentation at 
http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-ArrayLoader.html). 
This means that before you can load an array, you will need to have 
entered the manufacturer in the SRes.Contact (this can be done also 
via the StudyAnnotator Contact form) and you should have in RAD3.OntologyEntry 
an entry that describes the platform type. MGED has an ontology available 
that we use to populate RAD3.OntologyEntry for terms referring to 
platform types, namely the ontology for class=TechnologyType. The idea is 
that in RAD3.OntologyEntry we store the instances of this class, 
all of which have category set to 'TechnologyType". Similarly for 
SubstrateType, an array entry in RAD3.Array has a substrate_type_id that 
points to a term in RAd3.OntologyEntry describing the substrate type. For 
this we use the instances of the MGED SubstrateType class, that is we 
enter in RAD3.OntologyEntry an entry for each such instance, all having 
category set to "SubstrateType". To get the MGED instatnces (individuals) 
for TechnologyType and SubstrateType, you can go to 
http://mged.sourceforge.net/ontologies/MGEDontology.php#TechnologyType and 
http://mged.sourceforge.net/ontologies/MGEDontology.php#SubstrateType
I believe that, even though substrate_type_id is nullable in RAD3.Array, 
the ArrayLoader might require that this value is provided in the arguments 
anyway. Junmin, cc'ed in this email, can confirm this, as he is the author 
of the ArrayLoader plugin.
Elisabetta

On Fri, 14 Nov 2003, sam wang wrote:

> Dear friends,
> 
> after I download the new version of DbiDbHandle.pm,
> though it can go more steps, but there is no any data
> in my database, besides, there is an error "ERROR a
> VALID -- manufacturer_id must be on the commandline
> manufacturer_id = 0", I don't know the meaning and if
> it's the problem that I can't upload data? if so, how
> can I correct it?
> 
> Thank you very much for your help!
> Sammy
> 
> 
> please check the following error message:
> 
> [oracle@GUS oracle]$ ga GUS::RAD::Plugin::ArrayLoader
> --cfg_file
> /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> --data_file /home/oracle/RADDOTSdataset/assay5quan3
> --manufacturer_id 0 --platform_type_id 0
> Reading properties from
> /opt/gus/gus_home/config/GUS-PluginMgr.prop
> Reading properties from /home/oracle/.gus.properties
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> Fri Nov 14 19:43:23 2003 ALGINVID 3
> Fri Nov 14 19:43:23 2003 ARGS algoinvo 
> 1
> Fri Nov 14 19:43:23 2003 ARGS cfg_file 
> /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> Fri Nov 14 19:43:23 2003 ARGS comment
> Fri Nov 14 19:43:23 2003 ARGS commit
> Fri Nov 14 19:43:23 2003 ARGS data_file 
> /home/oracle/RADDOTSdataset/assay5quan3
> Fri Nov 14 19:43:23 2003 ARGS debug
> Fri Nov 14 19:43:23 2003 ARGS group
> Fri Nov 14 19:43:23 2003 ARGS gusconfigfile 
> /home/oracle/.gus.properties
> Fri Nov 14 19:43:23 2003 ARGS 
> manufacturer_id 0
> Fri Nov 14 19:43:23 2003 ARGS noWarning
> Fri Nov 14 19:43:23 2003 ARGS 
> platform_type_id 0
> Fri Nov 14 19:43:23 2003 ARGS project
> Fri Nov 14 19:43:23 2003 ARGS protocol_id
> Fri Nov 14 19:43:23 2003 ARGS restart
> Fri Nov 14 19:43:23 2003 ARGS sqlVerbose
> Fri Nov 14 19:43:23 2003 ARGS 
> substrate_type_id
> Fri Nov 14 19:43:23 2003 ARGS testnumber
> Fri Nov 14 19:43:23 2003 ARGS usage
> Fri Nov 14 19:43:23 2003 ARGS user
> Fri Nov 14 19:43:23 2003 ARGS verbose
> Fri Nov 14 19:43:23 2003 ARGS veryVerbose
> Fri Nov 14 19:43:23 2003 COMMIT commit off
> Fri Nov 14 19:43:23 2003 ERROR a VALID --
> manufacturer_id must be on the commandline
> manufacturer_id = 0
> Fri Nov 14 19:43:23 2003 RESULT
> [oracle@GUS oracle]$
> 
> 
> 
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-- 
Elisabetta Manduchi

Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1428 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021

phone: 215-573-4408
fax: 215 573-3111
email: man...@pc...
web: http://www.cbil.upenn.edu/~manduchi

---



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Re: [Gusdev-gusdev] Plugin to load plain fasta nucleotide sequences

[Steve F. <st...@pc...>]

sucheta-

take a look at the plugiun GUS::Common::Plugin::InsertNewExternalSequences

its in $PROJECT_HOME/GUS/Common/plugin/perl

steve

sucheta Tripathy wrote:

>I was wondering if there is a plugin to upload plain fasta  nucleotide
>sequences to GUS. This data is local and is not yet submitted to Genbank.
>
>Thanks
>
>Sucheta
>
>  
>

[Gusdev-gusdev] Plugin to load plain fasta nucleotide sequences

[sucheta T. <su...@vb...>]

I was wondering if there is a plugin to upload plain fasta  nucleotide
sequences to GUS. This data is local and is not yet submitted to Genbank.

Thanks

Sucheta

-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138

Re: [Gusdev-gusdev] about uploading RAD data problem

[Elisabetta M. <man...@pc...>]

Dear Sam,
regarding the part of your question referring to the manufacturer_id 
error, if you look at schemaBrowser for RAD3.Array at 
http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=RAD3::Array&path=RAD3::Array
you should see that manufacturer_id and platform_type_id are nonnullable. 
Thus a valid manufacturer_id and a valid platform_type_id must be given 
when running the ArrayLoader plugin (see also plugin documentation at 
http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-ArrayLoader.html). 
This means that before you can load an array, you will need to have 
entered the manufacturer in the SRes.Contact (this can be done also 
via the StudyAnnotator Contact form) and you should have in RAD3.OntologyEntry 
an entry that describes the platform type. MGED has an ontology available 
 that we use to populate RAD3.OntologyEntry for terms referring to 
platform types, namely the ontology for class=TechnologyType. The idea is 
that in RAD3.OntologyEntry we store the instances of this class, 
all of which have category set to 'TechnologyType". Similarly for 
SubstrateType, an array entry in RAD3.Array has a substrate_type_id that 
points to a term in RAd3.OntologyEntry describing the substrate type. For 
this we use the instances of the MGED SubstrateType class, that is we 
enter in RAD3.OntologyEntry an entry for each such instance, all having 
category set to "SubstrateType". To get the MGED instatnces (individuals) 
for TechnologyType and SubstrateType, you can go to 
http://mged.sourceforge.net/ontologies/MGEDontology.php#TechnologyType and 
http://mged.sourceforge.net/ontologies/MGEDontology.php#SubstrateType
I believe that, even though substrate_type_id is nullable in RAD3.Array, 
the ArrayLoader might require that this value is provided in the arguments 
anyway. Junmin, cc'ed in this email, can confirm this, as he is the author 
of the ArrayLoader plugin.
Elisabetta

On Fri, 14 Nov 2003, sam wang wrote:

> Dear friends,
> 
> after I download the new version of DbiDbHandle.pm,
> though it can go more steps, but there is no any data
> in my database, besides, there is an error "ERROR   a
> VALID -- manufacturer_id must be on the commandline
> manufacturer_id = 0", I don't know the meaning and if
> it's the problem that I can't upload data? if so, how
> can I correct it?
> 
> Thank you very much for your help!
> Sammy
> 
> 
> please check the following error message:
> 
> [oracle@GUS oracle]$ ga GUS::RAD::Plugin::ArrayLoader
> --cfg_file
> /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> --data_file /home/oracle/RADDOTSdataset/assay5quan3
> --manufacturer_id 0 --platform_type_id 0
> Reading properties from
> /opt/gus/gus_home/config/GUS-PluginMgr.prop
> Reading properties from /home/oracle/.gus.properties
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> ::st are not setup, RootClass ignored at
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
> Fri Nov 14 19:43:23 2003        ALGINVID        3
> Fri Nov 14 19:43:23 2003        ARGS    algoinvo      
>  1
> Fri Nov 14 19:43:23 2003        ARGS    cfg_file      
>  /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> Fri Nov 14 19:43:23 2003        ARGS    comment
> Fri Nov 14 19:43:23 2003        ARGS    commit
> Fri Nov 14 19:43:23 2003        ARGS    data_file     
>  /home/oracle/RADDOTSdataset/assay5quan3
> Fri Nov 14 19:43:23 2003        ARGS    debug
> Fri Nov 14 19:43:23 2003        ARGS    group
> Fri Nov 14 19:43:23 2003        ARGS    gusconfigfile 
>  /home/oracle/.gus.properties
> Fri Nov 14 19:43:23 2003        ARGS   
> manufacturer_id 0
> Fri Nov 14 19:43:23 2003        ARGS    noWarning
> Fri Nov 14 19:43:23 2003        ARGS   
> platform_type_id        0
> Fri Nov 14 19:43:23 2003        ARGS    project
> Fri Nov 14 19:43:23 2003        ARGS    protocol_id
> Fri Nov 14 19:43:23 2003        ARGS    restart
> Fri Nov 14 19:43:23 2003        ARGS    sqlVerbose
> Fri Nov 14 19:43:23 2003        ARGS   
> substrate_type_id
> Fri Nov 14 19:43:23 2003        ARGS    testnumber
> Fri Nov 14 19:43:23 2003        ARGS    usage
> Fri Nov 14 19:43:23 2003        ARGS    user
> Fri Nov 14 19:43:23 2003        ARGS    verbose
> Fri Nov 14 19:43:23 2003        ARGS    veryVerbose
> Fri Nov 14 19:43:23 2003        COMMIT  commit off
> Fri Nov 14 19:43:23 2003        ERROR   a VALID --
> manufacturer_id must be on the commandline
> manufacturer_id = 0
> Fri Nov 14 19:43:23 2003        RESULT
> [oracle@GUS oracle]$
> 
> 
> 
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-- 
Elisabetta Manduchi

Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1428 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021

phone: 215-573-4408
fax: 215 573-3111
email: man...@pc...
web: http://www.cbil.upenn.edu/~manduchi

---

[Gusdev-gusdev] about uploading RAD data problem

[sam w. <gus...@ya...>]

Dear friends,

after I download the new version of DbiDbHandle.pm,
though it can go more steps, but there is no any data
in my database, besides, there is an error "ERROR   a
VALID -- manufacturer_id must be on the commandline
manufacturer_id = 0", I don't know the meaning and if
it's the problem that I can't upload data? if so, how
can I correct it?

Thank you very much for your help!
Sammy


please check the following error message:

[oracle@GUS oracle]$ ga GUS::RAD::Plugin::ArrayLoader
--cfg_file
/opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
--data_file /home/oracle/RADDOTSdataset/assay5quan3
--manufacturer_id 0 --platform_type_id 0
Reading properties from
/opt/gus/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/oracle/.gus.properties
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
Fri Nov 14 19:43:23 2003        ALGINVID        3
Fri Nov 14 19:43:23 2003        ARGS    algoinvo      
 1
Fri Nov 14 19:43:23 2003        ARGS    cfg_file      
 /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
Fri Nov 14 19:43:23 2003        ARGS    comment
Fri Nov 14 19:43:23 2003        ARGS    commit
Fri Nov 14 19:43:23 2003        ARGS    data_file     
 /home/oracle/RADDOTSdataset/assay5quan3
Fri Nov 14 19:43:23 2003        ARGS    debug
Fri Nov 14 19:43:23 2003        ARGS    group
Fri Nov 14 19:43:23 2003        ARGS    gusconfigfile 
 /home/oracle/.gus.properties
Fri Nov 14 19:43:23 2003        ARGS   
manufacturer_id 0
Fri Nov 14 19:43:23 2003        ARGS    noWarning
Fri Nov 14 19:43:23 2003        ARGS   
platform_type_id        0
Fri Nov 14 19:43:23 2003        ARGS    project
Fri Nov 14 19:43:23 2003        ARGS    protocol_id
Fri Nov 14 19:43:23 2003        ARGS    restart
Fri Nov 14 19:43:23 2003        ARGS    sqlVerbose
Fri Nov 14 19:43:23 2003        ARGS   
substrate_type_id
Fri Nov 14 19:43:23 2003        ARGS    testnumber
Fri Nov 14 19:43:23 2003        ARGS    usage
Fri Nov 14 19:43:23 2003        ARGS    user
Fri Nov 14 19:43:23 2003        ARGS    verbose
Fri Nov 14 19:43:23 2003        ARGS    veryVerbose
Fri Nov 14 19:43:23 2003        COMMIT  commit off
Fri Nov 14 19:43:23 2003        ERROR   a VALID --
manufacturer_id must be on the commandline
manufacturer_id = 0
Fri Nov 14 19:43:23 2003        RESULT
[oracle@GUS oracle]$



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Re: [Gusdev-gusdev] SubmitRow: Can't locate object method "new" via package "GUS::Model::Sres::ExternalDatabase"

[Steve F. <sfi...@pc...>]

chetna-

the problem is that you misspelled SRes as 'Sres'

steve

Chetna Warade wrote:

>I am getting an error and my PERL5LIB looks okey:
>
>ga GUS::Common::Plugin::SubmitRow --tablename
>Sres::ExternalDatabase --attrlist
>"EXTERNAL_DATABASE_ID,NAME,LOWERCASE_NAME,MODIFICATION_DATE"
>--valuelist
>"1^^^'GenBank(nrdb)'^^^'genbank(nrdb)'^^^SYSDATE"
>--verbose
>Reading properties from
>/var/local/gus_home/config/GUS-PluginMgr.prop
>Reading properties from /home/chetna/.gus.properties
>
>Wed Nov 12 12:41:14 2003        ALGINVID        6
>Wed Nov 12 12:41:14 2003        COMMIT  commit off
>Can't locate object method "new" via package
>"GUS::Model::Sres::ExternalDatabase" (perhaps you
>forgot to load "GUS::Model::Sres::ExternalDatabase"?)
>at
>/var/local/gus_home/lib/perl/GUS/Common/Plugin/SubmitRow.pm
>line 104.
>
>Thanks for the help,
>Chetna
>
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[Gusdev-gusdev] SubmitRow: Can't locate object method "new" via package "GUS::Model::Sres::ExternalDatabase"

[Chetna W. <wa...@ya...>]

I am getting an error and my PERL5LIB looks okey:

ga GUS::Common::Plugin::SubmitRow --tablename
Sres::ExternalDatabase --attrlist
"EXTERNAL_DATABASE_ID,NAME,LOWERCASE_NAME,MODIFICATION_DATE"
--valuelist
"1^^^'GenBank(nrdb)'^^^'genbank(nrdb)'^^^SYSDATE"
--verbose
Reading properties from
/var/local/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/chetna/.gus.properties

Wed Nov 12 12:41:14 2003        ALGINVID        6
Wed Nov 12 12:41:14 2003        COMMIT  commit off
Can't locate object method "new" via package
"GUS::Model::Sres::ExternalDatabase" (perhaps you
forgot to load "GUS::Model::Sres::ExternalDatabase"?)
at
/var/local/gus_home/lib/perl/GUS/Common/Plugin/SubmitRow.pm
line 104.

Thanks for the help,
Chetna

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[Gusdev-gusdev] plugins speed difference due to dsn string

[Fidel S. <fi...@vb...>]

Hi folks!

This message is mostly with the hope that it may be of benefit
to those experiencing performance issues running plugins.  I also
ask two questions at the end related to implementation of the
plugins, specifically the SubmitRow plugin.

We had been experiencing performance issues when running plugins
and discovered that it was because of the dbiDsn string we were
using in the .gus.properties file.

First, let me describe our environment:
Our oracle is 9i with the server running on a big Sun machine
and the client running on linux, with following:
DBD::Oracle : 1.14
        DBI : 1.38
         OS : linux
       Perl : 5.008

The dbiDsn causing the slow performance follows the same form as
the one found in the gus.properties.sample in the GUS distribution
(in install directory).  In our case, that dbiDsn is:
dbiDsn=dbi:Oracle:host=tuor.bioinformatics.vt.edu;sid=gusdev

Following is the result of profiling the following call:
ga GUS::Common::Plugin::SubmitRow --tablename SRes::ExternalDatabase\
 --attrlist external_database_id,name,lowercase_name\
 --valuelist "200^^^GenBank(main)^^^genbank(main)"
 
Total Elapsed Time = 757.1146 Seconds
  User+System Time = 0.484621 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 12.3   0.060  0.208     11   0.0054 0.0189  GUS::PluginMgr::GusApplication::BEGIN
 8.25   0.040  0.040      4   0.0100 0.0100  DBD::Oracle::db::_login
 6.19   0.030  0.050      3   0.0100 0.0166  GUS::Model::Core::Algorithm_Row::BEGIN
 6.19   0.030  0.021    914   0.0000 0.0000  GUS::ObjRelP::DbiTable::getFullClassName
 6.19   0.030  0.039      5   0.0059 0.0078  GUS::ObjRelP::DbiDbHandle::BEGIN
 4.13   0.020  0.020      3   0.0067 0.0067  DynaLoader::dl_load_file
 4.13   0.020  0.020     37   0.0005 0.0005  DBI::_setup_handle
 4.13   0.020  0.020     28   0.0007 0.0007  DBI::st::execute
 4.13   0.020  0.020      6   0.0033 0.0033  GUS::Model::GusRow::BEGIN
 4.13   0.020  0.078     37   0.0005 0.0021  GUS::ObjRelP::DbiDatabase::getTable
 4.13   0.020  0.042     11   0.0018 0.0038  GUS::ObjRelP::DbiTable::BEGIN
 4.13   0.020  0.238      3   0.0067 0.0793  main::BEGIN
 4.13   0.020  0.069      4   0.0050 0.0173  GUS::ObjRelP::DbiDatabase::BEGIN
 3.71   0.018  0.026      1   0.0183 0.0264  GUS::ObjRelP::DbiDatabase::cacheTableNames
 2.06   0.010  0.008    870   0.0000 0.0000  DBI::st::fetchrow_array

When I change the dbiDsn string to:
dbiDsn=dbi:Oracle:gusdev.bioinformatics.vt.edu
profiling results in:

Total Elapsed Time = 1.104655 Seconds
  User+System Time = 0.534655 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 11.2   0.060  0.055   2470   0.0000 0.0000  GUS::ObjRelP::DbiRow::getTable
 7.48   0.040  0.050      3   0.0133 0.0166  GUS::Model::Core::Algorithm_Row::BEGIN
 7.48   0.040  0.208     11   0.0036 0.0189  GUS::PluginMgr::GusApplication::BEGIN
 5.61   0.030  0.030      4   0.0075 0.0075  DBD::Oracle::db::_login
 5.61   0.030  0.028    870   0.0000 0.0000  DBI::st::fetchrow_array
 5.61   0.030  0.084    951   0.0000 0.0001  GUS::ObjRelP::DbiDatabase::getFullTableClassName
 5.61   0.030  0.109     15   0.0020 0.0073  GUS::PluginMgr::Plugin::BEGIN
 5.61   0.030  0.118     37   0.0008 0.0032  GUS::ObjRelP::DbiDatabase::getTable
 5.61   0.030  0.039      5   0.0059 0.0078  GUS::ObjRelP::DbiDbHandle::BEGIN
 3.74   0.020  0.020      3   0.0067 0.0067  DynaLoader::dl_load_file
 3.74   0.020  0.238      3   0.0067 0.0793  main::BEGIN
 3.37   0.018  0.056      1   0.0183 0.0564  GUS::ObjRelP::DbiDatabase::cacheTableNames
 1.87   0.010  0.010     30   0.0003 0.0003  Exporter::import
 1.87   0.010  0.010     15   0.0007 0.0007  CBIL::Util::PropertySet::getProp
 1.87   0.010  0.010     37   0.0003 0.0003  DBI::st::TIEHASH

As you can see, that's a difference of > 12 minutes vs a little more than 1 second.

Question 1:
Now, looking at the profile results and walking over the code, I see that there are 
several connects made to the database (4 logins shown above) with the same parameters.
An obvious question, is why are several connections made?

Question 2:
Looking at the profiles above, does it make sense for such a simple submit row plugin
to make so many calls to GUS::ObjRelP::DbiRow::getTable, DBI::st::fetchrow_array,
GUS::ObjRelP::DbiDatabase::getFullTableClassName, and others?

Regards

Fidel

[Gusdev-gusdev] how to upload dataset of 'RAD' and 'DoTS' ? many thanks in advance!

[sam w. <gus...@ya...>]

Hi, friends,

does there anyone who know how to upload dataset of
'RAD' and 'DoTS' into database? when I first want to
upload dataset using ArrayLoader plugin of 'RAD', I
got the error information that I didn't register it.
so I tried register ArrayLoader plugin of 'RAD'
according to the command suggestion. but I got the
error information of: DBI subclasses
'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
setup.  
but I don't know what's that meaning, and how should I
setup that parameters. please check the error
information in detail at the bottom of this email,
besides, do you know how can I upload DoTS dataset to
database?


thank you very much for your great help in advance!
Sammy




the following is the error information:


[oracle@GUS perl]$ ga GUS::RAD::Plugin::ArrayLoader
--cfg_file
/opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
--data_file /home/oracle/RADDOTSdataset/assay5quan3
--manufacturer_id 0 --platform_type_id 0
Reading properties from
/opt/gus/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/oracle/.gus.properties
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
 
USER ERROR: GUS::RAD::Plugin::ArrayLoader has never
been registered.
Please use 'ga +create GUS::RAD::Plugin::ArrayLoader
--commit'
Issuing rollback() for database handle being DESTROY'd
without explicit disconnect().
[oracle@GUS perl]$ ga +create
GUS::RAD::Plugin::ArrayLoader --commit
Reading properties from
/opt/gus/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/oracle/.gus.properties
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
Sat Nov  8 23:46:18 2003        INFO    Plugin
GUS::RAD::Plugin::ArrayLoader registered with cvs
revision '1.4' and cvs tag ' '
[oracle@GUS perl]$



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Re: [Gusdev-gusdev] how to upload dataset of 'RAD' and 'DoTS' ? many thanks in advance!

[Elisabetta M. <man...@pc...>]

Dear Sam,
regarding your question on RAD data loading:

> sorry for the long error information. in a word, I
> don't know how can I upload 'RAD' data even though I
> found there several plugins for uploading 'RAD'
> dataset. besides, I don't know if I should use
> 'ArrayLoader' plugin to upload dataset download from
> the following webpage:
> http://www.cbil.upenn.edu/RAD3/php/download.php#study5
> because I saw there are totally six differents plugins
> in 'RAD'. I don't know which plugin should upload
> which data, in fact, I just find the above link about
> RAD dataset. and I don't know if there are some other
> datasets that can be downloaded from the website.

the RAD pipeline for how data should be loaded is summarized at the 
bottom of this email.
NOTE 1: We are currently working on a plugin that will enable batch 
loading for step 6. 
NOTE 2: The RAD Study-Annotator is available from a tarball that includes 
a README file and various dumps (see 
http://www.cbil.upenn.edu/RAD/RAD-installation.htm) and proper usage of 
the forms is described in a suite of tutorials at 
https://www.cbil.upenn.edu/RAD/tutorial/index.html.
NOTE 3: individual plugin documentation is at the gusdb website.
---
RAD Data Loading Pipeline (as of October 2003)

1. Array is loaded via ArrayLoader.pm, if not already in RAD.
2. User creates a new Study in RAD using the appropriate Study form in 
the StudyAnnotator.
3. Images and quantified data files are provided via CD or ftp. These 
files are archived on in appropriate directories for the study of 
interest.
4. A file on our web server mapping studies to their uris for images and 
quantified data is updated, with the info for this study. This file is 
subsequently used in the StudyAnnotator to link acquisitions and 
quantifications to the archived files.
5. Annotation for this study is done via the StudyAnnotator.
6. The quantified data are loaded into RAD via ArrayResultLoader.pm, 
after appropriate parsing.
7. At this point, if available, files with preprocessed (e.g. 
normalized, averaged, etc.) data can be loaded in RAD via (possibly 
repeated uses of) ProcessedResultLoader.pm.
8. If available, analysis result files are loaded via 
AnalysisResultLoader.pm. New views of RAD3::AnalysisResultImp can be 
created to accomodate new analysis protocols.
---

Re: [Gusdev-gusdev] how to upload dataset of 'RAD' and 'DoTS' ? many thanks in advance!

[Steve F. <st...@pc...>]

dear sam-
 
see below.

steve

sam wang wrote:

>Dear friends,
>
>I have installed GUS successfully and registed 'ga'
>and 'SubmitRow' plugin. now I want to upload data of
>'RAD' and 'DoTS'. but when I use 'ga' to upload data
>of 'RAD', I met the following problem,
>first, I don't know if I need register 'ArrayLoader'
>plugin. when I tried to register it using the
>following command, I got the errors as follow:
>
>
>[oracle@GUS perl]$ ga +create
>GUS::RAD::Plugin:ArrayLoader --verbose
>
i believe the syntax error it is referring to is that you are missing a 
':'  in the line above, after 'Plugin:'

>Reading properties from
>/opt/gus/gus_home/config/GUS-PluginMgr.prop
>Reading properties from /home/oracle/.gus.properties
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
> 
>ERROR: syntax error at (eval 3) line 1, near "require
>GUS::RAD::Plugin:"
> 
> 
>--------------------------- STACK TRACE
>-------------------------
>       
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','syntax
>error at (eval 3) line 1, near "require
>GUS::RAD::Plug...') called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 248
>       
>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 664
>       
>GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d00c)',0,'GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 456
>       
>GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 283
>       
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 192
>       
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060680)')
>called at /opt/gus/gus_home/bin/ga line 11
>
>
>
>
>if I ignore this error and try to upload data file,
>then I got the following errors:
>[oracle@GUS perl]$ ga GUS::RAD::Plugin:ArrayLoader
>--cfg_file
>/opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
>--data_file /home/oracle/RADDOTSdataset/assay5quan3
>Reading properties from
>/opt/gus/gus_home/config/GUS-PluginMgr.prop
> 
>ERROR: syntax error at (eval 1) line 1, near "require
>GUS::RAD::Plugin:"
> 
> 
>--------------------------- STACK TRACE
>-------------------------
>       
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','syntax
>error at (eval 1) line 1, near "require
>GUS::RAD::Plug...') called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 248
>       
>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 377
>       
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 283
>       
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
>called at
>/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 192
>       
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060680)')
>called at /opt/gus/gus_home/bin/ga line 11
>
>
>sorry for the long error information. in a word, I
>don't know how can I upload 'RAD' data even though I
>found there several plugins for uploading 'RAD'
>dataset. besides, I don't know if I should use
>'ArrayLoader' plugin to upload dataset download from
>the following webpage:
>http://www.cbil.upenn.edu/RAD3/php/download.php#study5
>because I saw there are totally six differents plugins
>in 'RAD'. I don't know which plugin should upload
>which data, in fact, I just find the above link about
>RAD dataset. and I don't know if there are some other
>datasets that can be downloaded from the website.
>
>as for 'DoTS', it seems worse than 'RAD', because I
>can't find any plugin to upload the dataset to GUS. 
>
>does anyone upload dataset of 'RAD' and 'DoTS' before?
>or does any document about how to upload dataset about
>'RAD' and 'DoTS'? any hint will be greatly appreciate!
>
>best wishes!
>Sammy
>
>
>
>__________________________________
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>
>-------------------------------------------------------
>This SF.Net email sponsored by: ApacheCon 2003,
>16-19 November in Las Vegas. Learn firsthand the latest
>developments in Apache, PHP, Perl, XML, Java, MySQL,
>WebDAV, and more! http://www.apachecon.com/
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>  
>

[Gusdev-gusdev] how to upload dataset of 'RAD' and 'DoTS' ? many thanks in advance!

[sam w. <gus...@ya...>]

Dear friends,

I have installed GUS successfully and registed 'ga'
and 'SubmitRow' plugin. now I want to upload data of
'RAD' and 'DoTS'. but when I use 'ga' to upload data
of 'RAD', I met the following problem,
first, I don't know if I need register 'ArrayLoader'
plugin. when I tried to register it using the
following command, I got the errors as follow:


[oracle@GUS perl]$ ga +create
GUS::RAD::Plugin:ArrayLoader --verbose
Reading properties from
/opt/gus/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/oracle/.gus.properties
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
 
ERROR: syntax error at (eval 3) line 1, near "require
GUS::RAD::Plugin:"
 
 
--------------------------- STACK TRACE
-------------------------
       
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','syntax
error at (eval 3) line 1, near "require
GUS::RAD::Plug...') called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 248
       
GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 664
       
GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d00c)',0,'GUS::RAD::Plugin:ArrayLoader')
called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 456
       
GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 283
       
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 192
       
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060680)')
called at /opt/gus/gus_home/bin/ga line 11




if I ignore this error and try to upload data file,
then I got the following errors:
[oracle@GUS perl]$ ga GUS::RAD::Plugin:ArrayLoader
--cfg_file
/opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
--data_file /home/oracle/RADDOTSdataset/assay5quan3
Reading properties from
/opt/gus/gus_home/config/GUS-PluginMgr.prop
 
ERROR: syntax error at (eval 1) line 1, near "require
GUS::RAD::Plugin:"
 
 
--------------------------- STACK TRACE
-------------------------
       
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','syntax
error at (eval 1) line 1, near "require
GUS::RAD::Plug...') called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 248
       
GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 377
       
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 283
       
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::RAD::Plugin:ArrayLoader')
called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 192
       
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060680)')
called at /opt/gus/gus_home/bin/ga line 11


sorry for the long error information. in a word, I
don't know how can I upload 'RAD' data even though I
found there several plugins for uploading 'RAD'
dataset. besides, I don't know if I should use
'ArrayLoader' plugin to upload dataset download from
the following webpage:
http://www.cbil.upenn.edu/RAD3/php/download.php#study5
because I saw there are totally six differents plugins
in 'RAD'. I don't know which plugin should upload
which data, in fact, I just find the above link about
RAD dataset. and I don't know if there are some other
datasets that can be downloaded from the website.

as for 'DoTS', it seems worse than 'RAD', because I
can't find any plugin to upload the dataset to GUS. 

does anyone upload dataset of 'RAD' and 'DoTS' before?
or does any document about how to upload dataset about
'RAD' and 'DoTS'? any hint will be greatly appreciate!

best wishes!
Sammy



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[Gusdev-gusdev] SubmitRow error

[sucheta T. <su...@vb...>]

We have been trying to upload some values using the SubmitRow plugin of
GUS using the following command,

ga GUS::Common::Plugin::SubmitRow --tablename SRes::ExternalDatabase
--attrlist
'external_database_id','name','lowercase_name','modification_date','user_read','user_write','group_read','group_write','other_read','other_write','row_user_id','row_group_id','row_project_id','row_alg_invocation_id'
--valuelist
"2^^^'GenBank(nrdb)'^^^'genbank(nrdb)'^^^SYSDATE^^^1^^^1^^^1^^^1^^^1^^^0^^^6^^^3^^^2^^^1"
--user sres

It gives us insufficient privilege error.
Reading properties from /home/apps/gus/gushome/config/GUS-PluginMgr.prop
Reading properties from /home/apps/gus/.gus.properties
Wed Nov  5 15:26:14 2003        ALGINVID        4
Wed Nov  5 15:26:14 2003        COMMIT  commit off
Insufficient permissions to update GUS::Model::SRes::ExternalDatabase 2
Wed Nov  5 15:26:14 2003        Row updated
Wed Nov  5 15:26:14 2003        RESULT  Updated one row

Can anyone comment on this.

Sucheta

-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138

Re: [Gusdev-gusdev] error uploading Genbank files

[Steve F. <sfi...@pc...>]

it seems that the genbank parser has a dependency on Parse::Yapp.

This module is available from CPAN 
http://www.cpan.org/modules/01modules.index.html

search that page for yapp to find the download file.

install it in a place that is within your perl path

steve

sucheta Tripathy wrote:

>Hi,
>
>We have been trying to upload the Genbank data on "trypanosoma cruzi"
>using the following option:
>
>ga GUS::Common::Plugin::GBParser
>--file=/usr/local/src/gus-related/tcruzi.genbank --debug --gbRel=135
>--db_rel_id=1
>
>Prior to this we populated the sres.externaldatabase and
>sres.externaldatabaserelease using the values from Chetna's document
>
>We got the following error which was followed by a number of other errors:
>--------------------------------------------------------------------------
>
>ERR     LINE=30 unrequireable class     Features        Can't locate
>Parse/Yapp/Driver.pm in @INC (@INC contains: /home/apps
>/gus/gushome/lib/perl /usr/lib/perl5/5.8.0/i486-linux /usr/lib/perl5/5.8.0
>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/li
>b/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl .) at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN
>0> line 92.
>BEGIN failed--compilation aborted at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN0>
>line 92.
>Compilation failed in require at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
>line 92.
>BEGIN failed--compilation aborted at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
>line 92.
>Compilation failed in require at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
><GEN0> line 92.
>BEGIN failed--compilation aborted at
>/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
><GEN0> line 92.
>Compilation failed in require at (eval 33) line 3, <GEN0> line 92.
>
>The file Parse/Yapp/Driver.pm was not found anywhere.
>
>Thanks in advance
>
>Sucheta
>
>
>  
>

[Gusdev-gusdev] error uploading Genbank files

[sucheta T. <su...@vb...>]

Hi,

We have been trying to upload the Genbank data on "trypanosoma cruzi"
using the following option:

ga GUS::Common::Plugin::GBParser
--file=/usr/local/src/gus-related/tcruzi.genbank --debug --gbRel=135
--db_rel_id=1

Prior to this we populated the sres.externaldatabase and
sres.externaldatabaserelease using the values from Chetna's document

We got the following error which was followed by a number of other errors:
--------------------------------------------------------------------------

ERR     LINE=30 unrequireable class     Features        Can't locate
Parse/Yapp/Driver.pm in @INC (@INC contains: /home/apps
/gus/gushome/lib/perl /usr/lib/perl5/5.8.0/i486-linux /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/li
b/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl .) at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN
0> line 92.
BEGIN failed--compilation aborted at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Loc.pm line 15, <GEN0>
line 92.
Compilation failed in require at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
line 92.
BEGIN failed--compilation aborted at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Feature.pm line 7, <GEN0>
line 92.
Compilation failed in require at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
<GEN0> line 92.
BEGIN failed--compilation aborted at
/home/apps/gus/gushome/lib/perl/CBIL/Bio/GenBank/Features.pm line 6,
<GEN0> line 92.
Compilation failed in require at (eval 33) line 3, <GEN0> line 92.

The file Parse/Yapp/Driver.pm was not found anywhere.

Thanks in advance

Sucheta


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138