gusdev-gusdev — Topics concerning GUS development

[GUSDEV] schema documentation ( and the plugins), revisited

[Josef J. <ju...@cs...>]

I have been working with the InsertSequenceFeatures
plugin and it has been invaluable towards understanding
the intended use of the schema.

The provided genbank2gus.xml file is in itself, quite a
useful piece of schema documentation, however it only
documents tables which are views on NAFeatureImp.

Is there such a document for views on AAFeatureImp?
If not, does anyone have similar documentation on
AAFeature tables?

Thank you for your help;


Josef


Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [GUSDEV] Initial installation

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

Chris-

The application framework is used primarily to load data into GUS.  
There is a separate Web Development Kit that is used to rapidly develop 
a website that offers users queries against the data.

The application framework runs out of a directory called $GUS_HOME.  It 
just needs to be accessible to whomever will be using it.  It can run on 
any machine that has access to the database server.  We typically 
reserve entire machines for our db servers for performance reasons.   
The application framework, on the other hand, is very light weight to 
install.  You can either install a single $GUS_HOME in a shared file 
system, or, you can install separate copies in individual home directories.

i hope that helps a little,
steve



Chris Topinka wrote:

> I'm not sure I understand.  Does this mean that the app framework 
> requires it's own schema on the local db?  We have several different 
> research projects in different departments/organisms at hand.  Would 
> this indicate the need for a seperate application framework for each 
> of these?  I guess what we're eventually trying to accomplish is 
> setting up GUS as a core facility for any project in the University of 
> Missouri system.  Most of our data comes from a core sequencing 
> facility - maybe start with a single app framework installation for 
> this data and bring up other app frameworks for data that is 
> incorporated from other facilities? What did you mean by "most groups 
> have several
> users sharing a single GUS database"?  Can you give an example?
>
> I've tried to read as much of the documentation as possible.  Can you 
> direct me to some information source that might help me out here?
>
> Thanks,
>
> Chris
> On 9/16/05, *Michael Saffitz* <msa...@pc... 
> <mailto:msa...@pc...> > wrote:
>
>
>     Hi Chris,
>
>     On 9/16/05 7:29 PM, "Chris Topinka" < cmt...@gm...
>     <mailto:cmt...@gm...>> wrote:
>
>     > The documentation suggests installing the schema and app
>     framework at the
>     > same time using:
>     >
>     > build GUS install -append -installDBSchema
>     >
>     > will
>     >
>     > build GUS install -installDBSchema
>     >
>     > work to create the database only?
>
>     No, the "build GUS install" command will always install the app
>     framework.
>
>     > Why would you want to install the app
>     > framework on a machine that is serving your database?
>
>     You don't necessarily need to install the app framework on your
>     database
>     server using the above command.  For example, I have a remote database
>     configured in the gus.config file.  -installDBSchema connects to
>     the remote
>     database to install/load the schema there, and installs the app
>     framework on
>     the local database.
>
>     > Is this a good idea?
>
>     If you're the only one using GUS, it may be perfectly fine to have
>     the app
>     framework on the same machine as the database, but most groups
>     have several
>     users sharing a single GUS database, and consequently don't have
>     the app
>     framework on the DB server.
>
>     > Is the app framework suitable to be run in a distributed fashion?
>
>     I'm not sure exactly what you mean by this... The app framework
>     isn't really
>     designed for a distributed environment beyond support for remote
>     databases.
>
>     > Can a
>     > single app framework installation connect many users to the
>     database?
>
>     In theory, yes, but in most cases each app framework has an
>     individual's
>     configuration such that as they load data, data provenance issues and
>     permissions can be handled and tracked appropriately.
>
>
>     > I ask this because the documentation says that many users (each
>     with their
>     > own installation of the Application Framework) will share the
>     database.
>     >
>     > When I install the app framework on other machines can I use:
>     >
>     > build GUS install -append
>     >
>     > to do this?
>
>     Yes.
>
>     >
>     > Thanks,
>     >
>     > Chris
>
>
>
>
>
> -- 
> Christopher M. Topinka
> NLM-BHIRT Predoctoral Fellow in Computer Science
> 113 Life Sciences Center
> University of Missouri
> Columbia, MO 65211
> (573)-823-0616
> cmt...@mi... <mailto:cmt...@mi...> 

Re: [GUSDEV] Initial installation

[Chris T. <cmt...@gm...>]

I'm not sure I understand. Does this mean that the app framework requires=
=20
it's own schema on the local db? We have several different research project=
s=20
in different departments/organisms at hand. Would this indicate the need fo=
r=20
a seperate application framework for each of these? I guess what we're=20
eventually trying to accomplish is setting up GUS as a core facility for an=
y=20
project in the University of Missouri system. Most of our data comes from a=
=20
core sequencing facility - maybe start with a single app framework=20
installation for this data and bring up other app frameworks for data that=
=20
is incorporated from other facilities? What did you mean by "most groups=20
have several
users sharing a single GUS database"? Can you give an example?

I've tried to read as much of the documentation as possible. Can you direct=
=20
me to some information source that might help me out here?

Thanks,

Chris
On 9/16/05, Michael Saffitz <msa...@pc... > wrote:
>=20
>=20
> Hi Chris,
>=20
> On 9/16/05 7:29 PM, "Chris Topinka" < cmt...@gm...> wrote:
>=20
> > The documentation suggests installing the schema and app framework at=
=20
> the
> > same time using:
> >
> > build GUS install -append -installDBSchema
> >
> > will=20
> >
> > build GUS install -installDBSchema
> >
> > work to create the database only?
>=20
> No, the "build GUS install" command will always install the app framework=
.
>=20
> > Why would you want to install the app=20
> > framework on a machine that is serving your database?
>=20
> You don't necessarily need to install the app framework on your database
> server using the above command. For example, I have a remote database
> configured in the gus.config file. -installDBSchema connects to the remot=
e
> database to install/load the schema there, and installs the app framework=
=20
> on
> the local database.
>=20
> > Is this a good idea?
>=20
> If you're the only one using GUS, it may be perfectly fine to have the ap=
p=20
>=20
> framework on the same machine as the database, but most groups have=20
> several
> users sharing a single GUS database, and consequently don't have the app
> framework on the DB server.
>=20
> > Is the app framework suitable to be run in a distributed fashion?=20
>=20
> I'm not sure exactly what you mean by this... The app framework isn't=20
> really
> designed for a distributed environment beyond support for remote=20
> databases.
>=20
> > Can a
> > single app framework installation connect many users to the database?=
=20
>=20
> In theory, yes, but in most cases each app framework has an individual's
> configuration such that as they load data, data provenance issues and
> permissions can be handled and tracked appropriately.
>=20
>=20
> > I ask this because the documentation says that many users (each with=20
> their
> > own installation of the Application Framework) will share the database.
> >
> > When I install the app framework on other machines can I use:=20
> >
> > build GUS install -append
> >
> > to do this?
>=20
> Yes.
>=20
> >
> > Thanks,
> >
> > Chris
>=20
>=20
>=20


--=20
Christopher M. Topinka
NLM-BHIRT Predoctoral Fellow in Computer Science=20
113 Life Sciences Center=20
University of Missouri
Columbia, MO 65211
(573)-823-0616
cmt...@mi...

Re: [GUSDEV] InsertSequenceFeatures

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

Adhemar-

You need to update all of $PROJECT_HOME/GUS/Supported, not just that one 
file.

steve

Adhemar Zerlotini Neto wrote:

> Hello
>
> I just downloaded the InsertSequenceFeatures plugin revision 3451 and 
> when I try to run it the following error appears:
>
> ERROR:
> Can't locate object method "ignoreFeature" via package 
> "GUS::Supported::BioperlFeatMapper" at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm 
> line 753, <GEN39> line 42.
>
> STACK TRACE:
>  at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm 
> line 753
>         
> GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x850b8cc)', 
> 'Bio::SeqFeature::Generic=HASH(0x9731c10)', 4) called at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm 
> line 728
>         
> GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x850b8cc)', 
> 'Bio::SeqFeature::Generic=HASH(0x9731c10)', 4) called at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm 
> line 368
>         
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x850b8cc)', 
> 'HASH(0x94c2c94)') called at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
> line 469
>         eval {...} called at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
> line 461
>         
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)', 
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
> line 380
>         
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)', 
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
> line 288
>         
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)', 
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at 
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
> line 197
>         
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)', 
> 'ARRAY(0x84e9918)') called at /usr/local/SchistoDB/gus_home/bin/ga line 11
>
>
> Do anybody know what is it about?
>
> Thanks
>
> Adhemar ------------------------------------------------------- SF.Net 
> email is sponsored by: Tame your development challenges with Apache's 
> Geronimo App Server. Download it for free - -and be entered to win a 
> 42" plasma tv or your very own Sony(tm)PSP. Click here to play: 
> http://sourceforge.net/geronimo.php 
> _______________________________________________ Gusdev-gusdev mailing 
> list Gus...@li... 
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev 

[GUSDEV] InsertSequenceFeatures

[Adhemar Z. N. <ad...@cp...>]

<font size=3D"1" style=3D"font-family: courier new,courier,monospace;"><s=
pan
style=3D"font-family: arial,helvetica,sans-serif;"><font size=3D"2">Hello=
<br
/><br />I just downloaded the InsertSequenceFeatures plugin revision 3451
and when I try to run it the following error appears:<br
/></font></span><br />ERROR:<br />Can't locate object method
&quot;ignoreFeature&quot; via package
&quot;GUS::Supported::BioperlFeatMapper&quot; at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 753, &lt;GEN39&gt; line 42.<br /><br />STACK TRACE:<br />=A0at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 753<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS=
::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x850b8cc)',
'Bio::SeqFeature::Generic=3DHASH(0x9731c10)', 4) called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 728<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Support=
ed::Plugin::InsertSequenceFeatures=3DHASH(0x850b8cc)',
'Bio::SeqFeature::Generic=3DHASH(0x9731c10)', 4) called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 368<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0x850b8cc)',
'HASH(0x94c2c94)') called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 469<br />=A0=A0=A0=A0=A0=A0=A0 eval {...} called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 461<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x84d5c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x84d5c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x84d5c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x84d5c20)',
'ARRAY(0x84e9918)') called at /usr/local/SchistoDB/gus_home/bin/ga line
11<br /><br /><br /><span style=3D"font-family:
arial,helvetica,sans-serif;"><font size=3D"2">Do anybody know what is it
about?<br /><br />Thanks<br /><br />Adhemar</font></span></font>

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[Jian Lu <jl...@vb...>]

Jennifer,

I did check other columns on GOSynonym. Most of the 'source_id' columns 
are empty, but 'text' are not, but they are the same as GOTerm's column 
'name' or 'definition' content. So if there is not a secondary 
identifier, why should its text be loaded into GOSynonym?

 
jld...@se... wrote:

>Jian,
>
>None of the rows created by the plugin should be empty.  Have you checked the
>'text' column?  Not every row will have a source_id because not everything
>entered into GOSynonym has a secondary identifier, but they should all have
>'text,' which is the column that holds the actual synonym.
>
>Jennifer
>
>Quoting Jian Lu <jl...@vb...>:
>
>  
>
>>Hi Jennifer,
>>
>>That makes sense now. It really helps understand this plugin.
>>
>>However, I have a new question, why the plugin loads so many empty 
>>records on SRes.GOSynonym while loading those secondary identifiers?
>>
>>
>>Thank you very much.
>>
>>Jian
>>
>>jld...@se... wrote:
>>
>>    
>>
>>>Jian,
>>>
>>>I beleive that the behavior we are observing is actually a designed
>>>      
>>>
>>behavior. 
>>    
>>
>>>The pattern that I observed in my last email indicated that everything that
>>>      
>>>
>>was
>>    
>>
>>>missing from the SRes.GOTerm table was a secondary identifier.  After
>>>      
>>>
>>further
>>    
>>
>>>investigation we noticed that secondary identifiers are stored in the
>>>SRes.GOSynonym table as source_ids.
>>>
>>>Please let us know if this resolves your problem, or if you encounter any
>>>further issues when dealing with the plugin.
>>>
>>>
>>>Jennifer
>>>
>>>Quoting Jian Lu <jl...@vb...>:
>>>
>>> 
>>>
>>>      
>>>
>>>>Steve,
>>>>
>>>>After further investigation of GO files and comparison of the database, 
>>>>here is the report:
>>>>
>>>>GO file information:
>>>>!autogenerated-by:     DAG-Edit version 1.419 rev 3
>>>>!saved-by:             gocvs
>>>>!date:                 Fri Aug 12 21:00:17 PDT 2005
>>>>!version: $Revision: 3.306 $
>>>>
>>>>unique GO terms in component.ontology: 1745
>>>>unique GO terms in function.ontology: 7902
>>>>unique GO terms in process.ontology: 10370
>>>>unique GO terms in all three files: 20015
>>>>
>>>>total loaded GO terms: 19395
>>>>total missing GO terms: 620
>>>>
>>>>
>>>>steve wrote:
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>>>jian-
>>>>>
>>>>>yes, we have used the plugin, but it has been changed a little 
>>>>>recently.  can you do a grep on the file to count how many terms there 
>>>>>are in it?   have you looked carefully at those entries in the file to 
>>>>>see if there is something that distinguishes them?    can you count 
>>>>>how many rows actually are in the database that were put there by that 
>>>>>run of the plugin?
>>>>>
>>>>>thanks for your help,
>>>>>steve
>>>>>
>>>>>Jian Lu wrote:
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>>>Hi group,
>>>>>>
>>>>>>I downloaded Gene Ontology version 3.306 
>>>>>>(component.ontology,function.ontology, process.ontology) and ran
>>>>>>GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
>>>>>>database.
>>>>>>Here is my command:
>>>>>>
>>>>>>ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
>>>>>>/home/data/ontology --functionExtDbName 'GO Function' 
>>>>>>--processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
>>>>>>--commit
>>>>>>
>>>>>>
>>>>>>Everything looks fine, no errors. It returned a result as "Created 
>>>>>>19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
>>>>>>entries in GOSynonym.  Skipped 0 total entries".
>>>>>>
>>>>>>But when I was doing other data checking, I found there are three GO 
>>>>>>terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
>>>>>>They do exist on the GO downloaded files.
>>>>>>Has anyone used this plugin to load GO and checked its completeness? 
>>>>>>Please advise. Thanks.
>>>>>>
>>>>>>Jian
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>-------------------------------------------------------
>>>>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
>>>>>>Practices
>>>>>>Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
>>>>>>& QA
>>>>>>Security * Process Improvement & Measurement * 
>>>>>>http://www.sqe.com/bsce5sf
>>>>>>_______________________________________________
>>>>>>Gusdev-gusdev mailing list
>>>>>>Gus...@li...
>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>
>>>
>>>-------------------------------------------------------
>>>SF.Net email is sponsored by:
>>>Tame your development challenges with Apache's Geronimo App Server. 
>>>Download it for free - -and be entered to win a 42" plasma tv or your very
>>>own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> 
>>>
>>>      
>>>
>>    
>>

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[<jld...@se...>]

Jian,

None of the rows created by the plugin should be empty.  Have you checked the
'text' column?  Not every row will have a source_id because not everything
entered into GOSynonym has a secondary identifier, but they should all have
'text,' which is the column that holds the actual synonym.

Jennifer

Quoting Jian Lu <jl...@vb...>:

> Hi Jennifer,
> 
> That makes sense now. It really helps understand this plugin.
> 
> However, I have a new question, why the plugin loads so many empty 
> records on SRes.GOSynonym while loading those secondary identifiers?
> 
> 
> Thank you very much.
> 
> Jian
> 
> jld...@se... wrote:
> 
> >Jian,
> >
> >I beleive that the behavior we are observing is actually a designed
> behavior. 
> >The pattern that I observed in my last email indicated that everything that
> was
> >missing from the SRes.GOTerm table was a secondary identifier.  After
> further
> >investigation we noticed that secondary identifiers are stored in the
> >SRes.GOSynonym table as source_ids.
> >
> >Please let us know if this resolves your problem, or if you encounter any
> >further issues when dealing with the plugin.
> >
> >
> >Jennifer
> >
> >Quoting Jian Lu <jl...@vb...>:
> >
> >  
> >
> >>Steve,
> >>
> >>After further investigation of GO files and comparison of the database, 
> >>here is the report:
> >>
> >>GO file information:
> >>!autogenerated-by:     DAG-Edit version 1.419 rev 3
> >>!saved-by:             gocvs
> >>!date:                 Fri Aug 12 21:00:17 PDT 2005
> >>!version: $Revision: 3.306 $
> >>
> >>unique GO terms in component.ontology: 1745
> >>unique GO terms in function.ontology: 7902
> >>unique GO terms in process.ontology: 10370
> >>unique GO terms in all three files: 20015
> >>
> >>total loaded GO terms: 19395
> >>total missing GO terms: 620
> >>
> >>
> >>steve wrote:
> >>
> >>    
> >>
> >>>jian-
> >>>
> >>>yes, we have used the plugin, but it has been changed a little 
> >>>recently.  can you do a grep on the file to count how many terms there 
> >>>are in it?   have you looked carefully at those entries in the file to 
> >>>see if there is something that distinguishes them?    can you count 
> >>>how many rows actually are in the database that were put there by that 
> >>>run of the plugin?
> >>>
> >>>thanks for your help,
> >>>steve
> >>>
> >>>Jian Lu wrote:
> >>>
> >>>      
> >>>
> >>>>Hi group,
> >>>>
> >>>>I downloaded Gene Ontology version 3.306 
> >>>>(component.ontology,function.ontology, process.ontology) and ran
> >>>>GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
> >>>>database.
> >>>>Here is my command:
> >>>>
> >>>>ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
> >>>>/home/data/ontology --functionExtDbName 'GO Function' 
> >>>>--processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
> >>>>--commit
> >>>>
> >>>>
> >>>>Everything looks fine, no errors. It returned a result as "Created 
> >>>>19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
> >>>>entries in GOSynonym.  Skipped 0 total entries".
> >>>>
> >>>>But when I was doing other data checking, I found there are three GO 
> >>>>terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
> >>>>They do exist on the GO downloaded files.
> >>>>Has anyone used this plugin to load GO and checked its completeness? 
> >>>>Please advise. Thanks.
> >>>>
> >>>>Jian
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
> >>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> >>>>Practices
> >>>>Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> >>>>& QA
> >>>>Security * Process Improvement & Measurement * 
> >>>>http://www.sqe.com/bsce5sf
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>        
> >>>>
> >>    
> >>
> >
> >
> >
> >
> >-------------------------------------------------------
> >SF.Net email is sponsored by:
> >Tame your development challenges with Apache's Geronimo App Server. 
> >Download it for free - -and be entered to win a 42" plasma tv or your very
> >own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >  
> >
> 
> 

Re: [GUSDEV] Initial installation

[Michael S. <msa...@pc...>]

Hi Chris,

On 9/16/05 7:29 PM, "Chris Topinka" <cmt...@gm...> wrote:

> The documentation suggests installing the schema and app framework at the
> same time using:
> 
> build GUS install -append -installDBSchema
> 
> will 
> 
> build GUS install -installDBSchema
> 
> work to create the database only?

No, the "build GUS install" command will always install the app framework.

> Why would you want to install the app
> framework on a machine that is serving your database?

You don't necessarily need to install the app framework on your database
server using the above command.  For example, I have a remote database
configured in the gus.config file.  -installDBSchema connects to the remote
database to install/load the schema there, and installs the app framework on
the local database.

> Is this a good idea?

If you're the only one using GUS, it may be perfectly fine to have the app
framework on the same machine as the database, but most groups have several
users sharing a single GUS database, and consequently don't have the app
framework on the DB server.

> Is the app framework suitable to be run in a distributed fashion?

I'm not sure exactly what you mean by this... The app framework isn't really
designed for a distributed environment beyond support for remote databases.

> Can a 
> single app framework installation connect many users to the database?

In theory, yes, but in most cases each app framework has an individual's
configuration such that as they load data, data provenance issues and
permissions can be handled and tracked appropriately.


> I ask this because the documentation says that many users (each with their
> own installation of the Application Framework) will share the database.
> 
> When I install the app framework on other machines can I use:
> 
> build GUS install -append
> 
> to do this?

Yes.

> 
> Thanks,
> 
> Chris

[GUSDEV] Initial installation

[Chris T. <cmt...@gm...>]

The documentation suggests installing the schema and app framework at the=
=20
same time using:

build GUS install -append -installDBSchema

will=20

build GUS install -installDBSchema=20

work to create the database only? Why would you want to install the app=20
framework on a machine that is serving your database? Is this a good idea?=
=20
Is the app framework suitable to be run in a distributed fashion? Can a=20
single app framework installation connect many users to the database?
I ask this because the documentation says that many users (each with their=
=20
own installation of the Application Framework) will share the database.=20

When I install the app framework on other machines can I use:

build GUS install -append

to do this?

Thanks,

Chris

--=20
Christopher M. Topinka
NLM-BHIRT Predoctoral Fellow in Computer Science
113 Life Sciences Center=20
University of Missouri
Columbia, MO 65211
(573)-823-0616
cmt...@mi...

RE: [GUSDEV] WDK 1.6 + GUS 3.5

[Y. T. G. <yg...@pc...>]

Yeah, that would be the next thing to check. Again, please refer to
"Installing the Toy View" section of the wiki document for how to do
this.
=20
-Thomas
=20
 -----Original Message-----
From: gus...@li...
[mailto:gus...@li...] On Behalf Of Mark
Heiges
Sent: Friday, September 16, 2005 5:10 PM
To: gus...@li...
Subject: Re: [GUSDEV] WDK 1.6 + GUS 3.5



Have you configured Tomcat to allow symbolic links as described in the
WDK doc?=20

On Sep 16, 2005, at 5:46 PM, Adhemar Zerlotini Neto wrote:



Hi again,

Correcting what I=B4ve said:

The WDK-Controller.jar is indeed in my webapp/WEB-INF/lib directory.
I ran the (jar -tf WDK-Controler.jar) and it seems to unpack some class
files. But the wdktoysite didn=B4t start yet and the tomcat log contains
the same error.=20

Sep 16, 2005 6:45:53 PM org.apache.catalina.core.StandardContext
listenerStart


SEVERE: Error configuring application listener of class
org.gusdb.wdk.controller.ApplicationInitListener


java.lang.ClassNotFoundException:
org.gusdb.wdk.controller.ApplicationInitListener


        at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader
.java:1337)


        at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader
.java:1186)





Adhemar

------------------------------------------------------- SF.Net email is
sponsored by: Tame your development challenges with Apache's Geronimo
App Server. Download it for free - -and be entered to win a 42" plasma
tv or your very own Sony(tm)PSP. Click here to play:
http://sourceforge.net/geronimo.php
_______________________________________________ Gusdev-gusdev mailing
list Gus...@li...
https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] WDK 1.6 + GUS 3.5

[Mark H. <mh...@ug...>]

Have you configured Tomcat to allow symbolic links as described in the =20=

WDK doc?

On Sep 16, 2005, at 5:46 PM, Adhemar Zerlotini Neto wrote:

>  Hi again,
>
> Correcting what I=B4ve said:
>
> The WDK-Controller.jar is indeed in my webapp/WEB-INF/lib directory.
> I ran the (jar -tf WDK-Controler.jar) and it seems to unpack some =20
> class files. But the wdktoysite didn=B4t start yet and the tomcat log =20=

> contains the same error.
>
> Sep 16, 2005 6:45:53 PM org.apache.catalina.core.StandardContext =20
> listenerStart
> SEVERE: Error configuring application listener of class =20
> org.gusdb.wdk.controller.ApplicationInitListener
> java.lang.ClassNotFoundException: =20
> org.gusdb.wdk.controller.ApplicationInitListener
> =A0=A0=A0=A0=A0=A0=A0 at =20
> =
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoade=20=

> r.java:1337)
> =A0=A0=A0=A0=A0=A0=A0 at =20
> =
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoade=20=

> r.java:1186)
>
>
>
> Adhemar
>
>  ------------------------------------------------------- SF.Net email =20=

> is sponsored by: Tame your development challenges with Apache's =20
> Geronimo App Server. Download it for free - -and be entered to win a =20=

> 42" plasma tv or your very own Sony(tm)PSP. Click here to play: =20
> http://sourceforge.net/geronimo.php =20
> _______________________________________________ Gusdev-gusdev mailing =20=

> list Gus...@li... =20
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev=

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[Jian Lu <jl...@vb...>]

Hi Jennifer,

That makes sense now. It really helps understand this plugin.

However, I have a new question, why the plugin loads so many empty 
records on SRes.GOSynonym while loading those secondary identifiers?


Thank you very much.

Jian

jld...@se... wrote:

>Jian,
>
>I beleive that the behavior we are observing is actually a designed behavior. 
>The pattern that I observed in my last email indicated that everything that was
>missing from the SRes.GOTerm table was a secondary identifier.  After further
>investigation we noticed that secondary identifiers are stored in the
>SRes.GOSynonym table as source_ids.
>
>Please let us know if this resolves your problem, or if you encounter any
>further issues when dealing with the plugin.
>
>
>Jennifer
>
>Quoting Jian Lu <jl...@vb...>:
>
>  
>
>>Steve,
>>
>>After further investigation of GO files and comparison of the database, 
>>here is the report:
>>
>>GO file information:
>>!autogenerated-by:     DAG-Edit version 1.419 rev 3
>>!saved-by:             gocvs
>>!date:                 Fri Aug 12 21:00:17 PDT 2005
>>!version: $Revision: 3.306 $
>>
>>unique GO terms in component.ontology: 1745
>>unique GO terms in function.ontology: 7902
>>unique GO terms in process.ontology: 10370
>>unique GO terms in all three files: 20015
>>
>>total loaded GO terms: 19395
>>total missing GO terms: 620
>>
>>
>>steve wrote:
>>
>>    
>>
>>>jian-
>>>
>>>yes, we have used the plugin, but it has been changed a little 
>>>recently.  can you do a grep on the file to count how many terms there 
>>>are in it?   have you looked carefully at those entries in the file to 
>>>see if there is something that distinguishes them?    can you count 
>>>how many rows actually are in the database that were put there by that 
>>>run of the plugin?
>>>
>>>thanks for your help,
>>>steve
>>>
>>>Jian Lu wrote:
>>>
>>>      
>>>
>>>>Hi group,
>>>>
>>>>I downloaded Gene Ontology version 3.306 
>>>>(component.ontology,function.ontology, process.ontology) and ran
>>>>GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
>>>>database.
>>>>Here is my command:
>>>>
>>>>ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
>>>>/home/data/ontology --functionExtDbName 'GO Function' 
>>>>--processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
>>>>--commit
>>>>
>>>>
>>>>Everything looks fine, no errors. It returned a result as "Created 
>>>>19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
>>>>entries in GOSynonym.  Skipped 0 total entries".
>>>>
>>>>But when I was doing other data checking, I found there are three GO 
>>>>terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
>>>>They do exist on the GO downloaded files.
>>>>Has anyone used this plugin to load GO and checked its completeness? 
>>>>Please advise. Thanks.
>>>>
>>>>Jian
>>>>
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
>>>>Practices
>>>>Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
>>>>& QA
>>>>Security * Process Improvement & Measurement * 
>>>>http://www.sqe.com/bsce5sf
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>        
>>>>
>>    
>>
>
>
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by:
>Tame your development challenges with Apache's Geronimo App Server. 
>Download it for free - -and be entered to win a 42" plasma tv or your very
>own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

RE: [GUSDEV] WDK 1.6 + GUS 3.5

[Y. T. G. <yg...@pc...>]

It appears that your install did not work. Please follow instructions at
this link carefully:
http://www.gusdb.org/wiki/index.php/Gus%20Wdk%201.6#Installingx20.thex20
.WDK
Pay special attention to the section "Installing the Toy View".=20
When you run "build WDKToySite webinstall -append -webPropFile
your_web_prop_file", you would
specify the target installation dir with the property
"webappTargetDir=3Dyour_webapp_directory"
and the build script will make a symbolic link under
your_webapp_directory/WEB-INF/lib
pointing to your $GUS_HOME/lib/java, where the WDK-Model and
WDK-Controller jar files
would have been created when you did "build WDK install -append" in an
earlier step.
=20
-Thomas
=20
 -----Original Message-----
From: gus...@li...
[mailto:gus...@li...] On Behalf Of Adhemar
Zerlotini Neto
Sent: Friday, September 16, 2005 4:25 PM
To: Y. Thomas Gan
Cc: gus...@li...
Subject: RE: [GUSDEV] WDK 1.6 + GUS 3.5



Hi Thomas,

I didn't find any of the .jar file you mentioned and I didn't also find
the controller directory.=20

Shouldn't this files been installed by the build script?
Were can I get a copy of them?

Thanks=20

Adhemar




> Hi Adhemar,
> Please verify that 1) your webapp/WEB-INF/lib contains
> WDK-Controller.jar and 2) this jar file contains the class
> org/gusdb/wdk/controller/ApplicationInitListener.class (jar -tf
> WDK-Controller.jar).
>=20
> -Thomas
>=20
> -----Original Message-----
> From: gus...@li...
> [mailto:gus...@li...] On Behalf Of
Adhemar
> Zerlotini Neto
> Sent: Friday, September 16, 2005 1:32 PM
> To: gus...@li...
> Subject: [GUSDEV] WDK 1.6 + GUS 3.5
>=20
>=20
>=20
>=20
> Hi everybody,
>=20
> I've been trying to install the wdktoysite to my gus instance but I've
> got a problem I can't solve.
>=20
> I'm following the wdk wiki steps to install the wdk but in the moment
of
> starting the tomcat the wdktoysite fails to start.
>=20
> I guess there's a missing class file based on the tomcat log. Here is
> part of the log file:
>=20
>=20
>=20
> Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext
> listenerStart
> SEVERE: Error configuring application listener of class
> org.gusdb.wdk.controller.ApplicationInitListener
> java.lang.ClassNotFoundException:
> org.gusdb.wdk.controller.ApplicationInitListener
> at
>
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader
> .java:1337)
> at
>
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader
> .java:1186)
> at
>
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.j
> ava:3640)
> at
>
org.apache.catalina.core.StandardContext.start(StandardContext.java:4127
> )
> at
>
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.ja
> va:759)
> at
>
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:739)
> at
> org.apache.catalina.core.StandardHost.addChild(StandardHost.java:524)
> at
>
org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:9
> 10)
> at
>
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java
> :873)
> at
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:474)
> at
> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1118)
> at
>
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:31
> 0)
> at
>
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSu
> pport.java:119)
> at
> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1020)
> at
> org.apache.catalina.core.StandardHost.start(StandardHost.java:718)
> at
> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1012)
> at
> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:442)
> at
>
org.apache.catalina.core.StandardService.start(StandardService.java:450)
> at
> org.apache.catalina.core.StandardServer.start(StandardServer.java:680)
> at org.apache.catalina.startup.Catalina.start(Catalina.java:540)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
>
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
> a:39)
> at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:585)
> at
> org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:271)
> at
> org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:409)
> Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext
> listenerStart
> SEVERE: Skipped installing application listeners due to previous
> error(s)
> Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext start
> SEVERE: Error listenerStart
> Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext start
> SEVERE: Context [/wdktoysite] startup failed due to previous errors
> Sep 16, 2005 3:26:33 PM org.apache.coyote.http11.Http11Protocol start
> INFO: Starting Coyote HTTP/1.1 on http-2020
>=20
>=20
>=20
> Can anyone send me a tip about this?
>=20
> Thanks in advance
>=20
> Adhemar
>=20
> ------------------------------------------------------- SF.Net email
is
> sponsored by: Tame your development challenges with Apache's Geronimo
> App Server. Download it for free - -and be entered to win a 42" plasma
> tv or your very own Sony(tm)PSP. Click here to play:
> http://sourceforge.net/geronimo.php
> _______________________________________________ Gusdev-gusdev mailing
> list Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>=20
>=20
> --
> Centro de Pesquisas Ren=E9 Rachou/CPqRR - A FIOCRUZ em Minas Gerais.
> Rene Rachou Research Center/CPqRR - The Oswaldo Cruz Foundation in the
> State of Minas Gerais-Brazil.
> http://www.cpqrr.fiocruz.br
>=20
>=20


Adhemar Zerlotini Neto
Centro de Pesquisas Ren=E9 Rachou - FIOCRUZ
Av. Augusto de Lima 1715
BH MG 30190-002, Brazil
Phone: +55-31-3349-7785
------------------------------------------------------- SF.Net email is
sponsored by: Tame your development challenges with Apache's Geronimo
App Server. Download it for free - -and be entered to win a 42" plasma
tv or your very own Sony(tm)PSP. Click here to play:
http://sourceforge.net/geronimo.php
_______________________________________________ Gusdev-gusdev mailing
list Gus...@li...
https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev=20

RE: [GUSDEV] WDK 1.6 + GUS 3.5

[Adhemar Z. N. <ad...@cp...>]

Hi again,<br /><br />Correcting what I=B4ve said:<br /><br />The
WDK-Controller.jar is indeed in my webapp/WEB-INF/lib directory.<br />I
ran the (jar -tf WDK-Controler.jar) and it seems to unpack some class
files. But the wdktoysite didn=B4t start yet and the tomcat log contains =
the
same error. <br /><br /><font size=3D"1" style=3D"font-family: courier
new,courier,monospace;">Sep 16, 2005 6:45:53 PM
org.apache.catalina.core.StandardContext listenerStart<br />SEVERE: Error
configuring application listener of class
org.gusdb.wdk.controller.ApplicationInitListener<br
/>java.lang.ClassNotFoundException:
org.gusdb.wdk.controller.ApplicationInitListener<br />=A0=A0=A0=A0=A0=A0=A0=
 at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.=
java:1337)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.=
java:1186)</font><br
/><br /><br /><br />Adhemar<br /><br />

RE: [GUSDEV] WDK 1.6 + GUS 3.5

[Adhemar Z. N. <ad...@cp...>]

Hi Thomas,<br /><br />I didn't find any of the .jar file you mentioned an=
d
I didn't also find the controller directory. <br /><br />Shouldn't this
files been installed by the build script?<br />Were can I get a copy of
them?<br /><br />Thanks <br /><br />Adhemar<br /><br /><br /><br /><br
/>&gt; Hi Adhemar,<br />&gt; Please verify that 1) your webapp/WEB-INF/li=
b
contains<br />&gt; WDK-Controller.jar and 2) this jar file contains the
class<br />&gt; org/gusdb/wdk/controller/ApplicationInitListener.class=20
(jar -tf<br />&gt; WDK-Controller.jar).<br />&gt; <br />&gt; -Thomas<br
/>&gt; <br />&gt;  -----Original Message-----<br />&gt; From:
gus...@li...<br />&gt;
[mailto:gus...@li...] On Behalf Of Adhemar<b=
r
/>&gt; Zerlotini Neto<br />&gt; Sent: Friday, September 16, 2005 1:32
PM<br />&gt; To: gus...@li...<br />&gt; Subject:
[GUSDEV] WDK 1.6 + GUS 3.5<br />&gt; <br />&gt; <br />&gt; <br />&gt; <br
/>&gt; Hi everybody,<br />&gt; <br />&gt; I've been trying to install the
wdktoysite to my gus instance but I've<br />&gt; got a problem I can't
solve.<br />&gt; <br />&gt; I'm following the wdk wiki steps to install
the wdk but in the moment of<br />&gt; starting the tomcat the wdktoysite
fails to start.<br />&gt; <br />&gt; I guess there's a missing class file
based on the tomcat log. Here is<br />&gt; part of the log file:<br />&gt=
;
<br />&gt; <br />&gt; <br />&gt; Sep 16, 2005 3:26:32 PM
org.apache.catalina.core.StandardContext<br />&gt; listenerStart<br />&gt=
;
SEVERE: Error configuring application listener of class<br />&gt;
org.gusdb.wdk.controller.ApplicationInitListener<br />&gt;
java.lang.ClassNotFoundException:<br />&gt;
org.gusdb.wdk.controller.ApplicationInitListener<br />&gt;         at<br
/>&gt;
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader<=
br
/>&gt; .java:1337)<br />&gt;         at<br />&gt;
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader<=
br
/>&gt; .java:1186)<br />&gt;         at<br />&gt;
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.j<=
br
/>&gt; ava:3640)<br />&gt;         at<br />&gt;
org.apache.catalina.core.StandardContext.start(StandardContext.java:4127<=
br
/>&gt; )<br />&gt;         at<br />&gt;
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.ja<=
br
/>&gt; va:759)<br />&gt;         at<br />&gt;
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:739)<b=
r
/>&gt;         at<br />&gt;
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:524)<br
/>&gt;         at<br />&gt;
org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:9<=
br
/>&gt; 10)<br />&gt;         at<br />&gt;
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java<=
br
/>&gt; :873)<br />&gt;         at<br />&gt;
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:474)<br
/>&gt;         at<br />&gt;
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1118)<br
/>&gt;         at<br />&gt;
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:31<=
br
/>&gt; 0)<br />&gt;         at<br />&gt;
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSu<=
br
/>&gt; pport.java:119)<br />&gt;         at<br />&gt;
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1020)<br
/>&gt;         at<br />&gt;
org.apache.catalina.core.StandardHost.start(StandardHost.java:718)<br
/>&gt;         at<br />&gt;
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1012)<br
/>&gt;         at<br />&gt;
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:442)<br
/>&gt;         at<br />&gt;
org.apache.catalina.core.StandardService.start(StandardService.java:450)<=
br
/>&gt;         at<br />&gt;
org.apache.catalina.core.StandardServer.start(StandardServer.java:680)<br
/>&gt;         at
org.apache.catalina.startup.Catalina.start(Catalina.java:540)<br />&gt;  =
=20
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br
/>&gt;         at<br />&gt;
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav<=
br
/>&gt; a:39)<br />&gt;         at<br />&gt;
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor<=
br
/>&gt; Impl.java:25)<br />&gt;         at
java.lang.reflect.Method.invoke(Method.java:585)<br />&gt;         at<br
/>&gt; org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:271)<br
/>&gt;         at<br />&gt;
org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:409)<br />&gt;
Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext<br />&gt=
;
listenerStart<br />&gt; SEVERE: Skipped installing application listeners
due to previous<br />&gt; error(s)<br />&gt; Sep 16, 2005 3:26:32 PM
org.apache.catalina.core.StandardContext start<br />&gt; SEVERE: Error
listenerStart<br />&gt; Sep 16, 2005 3:26:32 PM
org.apache.catalina.core.StandardContext start<br />&gt; SEVERE: Context
[/wdktoysite] startup failed due to previous errors<br />&gt; Sep 16, 200=
5
3:26:33 PM org.apache.coyote.http11.Http11Protocol start<br />&gt; INFO:
Starting Coyote HTTP/1.1 on http-2020<br />&gt; <br />&gt; <br />&gt; <br
/>&gt; Can anyone send me a tip about this?<br />&gt; <br />&gt; Thanks i=
n
advance<br />&gt; <br />&gt; Adhemar<br />&gt; <br />&gt;
------------------------------------------------------- SF.Net email is<b=
r
/>&gt; sponsored by: Tame your development challenges with Apache's
Geronimo<br />&gt; App Server. Download it for free - -and be entered to
win a 42&quot; plasma<br />&gt; tv or your very own Sony(tm)PSP. Click
here to play:<br />&gt; http://sourceforge.net/geronimo.php<br />&gt;
_______________________________________________ Gusdev-gusdev mailing<br
/>&gt; list Gus...@li...<br />&gt;
https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev<br />&gt; <br
/>&gt; <br />&gt; --<br />&gt; Centro de Pesquisas Ren=E9 Rachou/CPqRR - =
A
FIOCRUZ em Minas Gerais.<br />&gt; Rene Rachou Research Center/CPqRR - Th=
e
Oswaldo Cruz Foundation in the<br />&gt; State of Minas Gerais-Brazil.<br
/>&gt; http://www.cpqrr.fiocruz.br<br />&gt; <br />&gt; <br /><br /><br
/>Adhemar Zerlotini Neto<br />Centro de Pesquisas Ren=E9 Rachou - FIOCRUZ=
<br
/>Av. Augusto de Lima 1715<br />BH MG 30190-002, Brazil<br />Phone:
+55-31-3349-7785

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[<jld...@se...>]

Jian,

I beleive that the behavior we are observing is actually a designed behavior. 
The pattern that I observed in my last email indicated that everything that was
missing from the SRes.GOTerm table was a secondary identifier.  After further
investigation we noticed that secondary identifiers are stored in the
SRes.GOSynonym table as source_ids.

Please let us know if this resolves your problem, or if you encounter any
further issues when dealing with the plugin.


Jennifer

Quoting Jian Lu <jl...@vb...>:

> Steve,
> 
> After further investigation of GO files and comparison of the database, 
> here is the report:
> 
> GO file information:
> !autogenerated-by:     DAG-Edit version 1.419 rev 3
> !saved-by:             gocvs
> !date:                 Fri Aug 12 21:00:17 PDT 2005
> !version: $Revision: 3.306 $
> 
> unique GO terms in component.ontology: 1745
> unique GO terms in function.ontology: 7902
> unique GO terms in process.ontology: 10370
> unique GO terms in all three files: 20015
> 
> total loaded GO terms: 19395
> total missing GO terms: 620
> 
> 
> steve wrote:
> 
> > jian-
> >
> > yes, we have used the plugin, but it has been changed a little 
> > recently.  can you do a grep on the file to count how many terms there 
> > are in it?   have you looked carefully at those entries in the file to 
> > see if there is something that distinguishes them?    can you count 
> > how many rows actually are in the database that were put there by that 
> > run of the plugin?
> >
> > thanks for your help,
> > steve
> >
> > Jian Lu wrote:
> >
> >> Hi group,
> >>
> >> I downloaded Gene Ontology version 3.306 
> >> (component.ontology,function.ontology, process.ontology) and ran
> >> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
> >> database.
> >> Here is my command:
> >>
> >> ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
> >> /home/data/ontology --functionExtDbName 'GO Function' 
> >> --processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
> >> --commit
> >>
> >>
> >> Everything looks fine, no errors. It returned a result as "Created 
> >> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
> >> entries in GOSynonym.  Skipped 0 total entries".
> >>
> >> But when I was doing other data checking, I found there are three GO 
> >> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
> >> They do exist on the GO downloaded files.
> >> Has anyone used this plugin to load GO and checked its completeness? 
> >> Please advise. Thanks.
> >>
> >> Jian
> >>
> >>
> >>
> >>
> >> -------------------------------------------------------
> >> SF.Net email is Sponsored by the Better Software Conference & EXPO
> >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> >> Practices
> >> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> >> & QA
> >> Security * Process Improvement & Measurement * 
> >> http://www.sqe.com/bsce5sf
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
> 

RE: [GUSDEV] WDK 1.6 + GUS 3.5

[Y. T. G. <yg...@pc...>]

Hi Adhemar,
Please verify that 1) your webapp/WEB-INF/lib contains
WDK-Controller.jar and 2) this jar file contains the class
org/gusdb/wdk/controller/ApplicationInitListener.class  (jar -tf
WDK-Controller.jar).
 
-Thomas
 
 -----Original Message-----
From: gus...@li...
[mailto:gus...@li...] On Behalf Of Adhemar
Zerlotini Neto
Sent: Friday, September 16, 2005 1:32 PM
To: gus...@li...
Subject: [GUSDEV] WDK 1.6 + GUS 3.5




Hi everybody,

I've been trying to install the wdktoysite to my gus instance but I've
got a problem I can't solve.

I'm following the wdk wiki steps to install the wdk but in the moment of
starting the tomcat the wdktoysite fails to start. 

I guess there's a missing class file based on the tomcat log. Here is
part of the log file:



Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext
listenerStart
SEVERE: Error configuring application listener of class
org.gusdb.wdk.controller.ApplicationInitListener
java.lang.ClassNotFoundException:
org.gusdb.wdk.controller.ApplicationInitListener
        at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader
.java:1337)
        at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader
.java:1186)
        at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.j
ava:3640)
        at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4127
)
        at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.ja
va:759)
        at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:739)
        at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:524)
        at
org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:9
10)
        at
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java
:873)
        at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:474)
        at
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1118)
        at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:31
0)
        at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSu
pport.java:119)
        at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1020)
        at
org.apache.catalina.core.StandardHost.start(StandardHost.java:718)
        at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1012)
        at
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:442)
        at
org.apache.catalina.core.StandardService.start(StandardService.java:450)
        at
org.apache.catalina.core.StandardServer.start(StandardServer.java:680)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:540)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:39)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:271)
        at
org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:409)
Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext
listenerStart
SEVERE: Skipped installing application listeners due to previous
error(s)
Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Sep 16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [/wdktoysite] startup failed due to previous errors
Sep 16, 2005 3:26:33 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-2020



Can anyone send me a tip about this?

Thanks in advance

Adhemar

------------------------------------------------------- SF.Net email is
sponsored by: Tame your development challenges with Apache's Geronimo
App Server. Download it for free - -and be entered to win a 42" plasma
tv or your very own Sony(tm)PSP. Click here to play:
http://sourceforge.net/geronimo.php
_______________________________________________ Gusdev-gusdev mailing
list Gus...@li...
https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev 

[GUSDEV] WDK 1.6 + GUS 3.5

[Adhemar Z. N. <ad...@cp...>]

<font size=3D"1" style=3D"font-family: courier new,courier,monospace;"><b=
r
/><font size=3D"3"><span style=3D"font-family: arial,helvetica,sans-serif=
;">Hi
everybody,<br /><br />I've been trying to install the wdktoysite to my gu=
s
instance but I've got a problem I can't solve.<br /><br />I'm following
the wdk wiki steps to install the wdk but in the moment of starting the
tomcat the wdktoysite fails to start. <br /><br />I guess there's a
missing class file based on the tomcat log. Here is part of the log
file:<br /><br /></span></font><br /><br />Sep 16, 2005 3:26:32 PM
org.apache.catalina.core.StandardContext listenerStart<br />SEVERE: Error
configuring application listener of class
org.gusdb.wdk.controller.ApplicationInitListener<br
/>java.lang.ClassNotFoundException:
org.gusdb.wdk.controller.ApplicationInitListener<br />=A0=A0=A0=A0=A0=A0=A0=
 at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.=
java:1337)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.=
java:1186)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.ja=
va:3640)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4127)=
<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.jav=
a:759)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:739)<b=
r
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:524)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:91=
0)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:=
873)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:474)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1118)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:310=
)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSup=
port.java:119)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1020)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.StandardHost.start(StandardHost.java:718)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1012)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:442)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.StandardService.start(StandardService.java:450)<=
br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.core.StandardServer.start(StandardServer.java:680)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.startup.Catalina.start(Catalina.java:540)<br />=A0=A0=
=A0=A0=A0=A0=A0
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java=
:39)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorI=
mpl.java:25)<br
/>=A0=A0=A0=A0=A0=A0=A0 at java.lang.reflect.Method.invoke(Method.java:58=
5)<br />=A0=A0=A0=A0=A0=A0=A0
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:271)<br
/>=A0=A0=A0=A0=A0=A0=A0 at
org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:409)<br />Sep
16, 2005 3:26:32 PM org.apache.catalina.core.StandardContext
listenerStart<br />SEVERE: Skipped installing application listeners due t=
o
previous error(s)<br />Sep 16, 2005 3:26:32 PM
org.apache.catalina.core.StandardContext start<br />SEVERE: Error
listenerStart<br />Sep 16, 2005 3:26:32 PM
org.apache.catalina.core.StandardContext start<br />SEVERE: Context
[/wdktoysite] startup failed due to previous errors<br />Sep 16, 2005
3:26:33 PM org.apache.coyote.http11.Http11Protocol start<br />INFO:
Starting Coyote HTTP/1.1 on http-2020<br /><br /><span style=3D"font-fami=
ly:
arial,helvetica,sans-serif;"><font size=3D"2"><br /><br /><font size=3D"3=
">Can
anyone send me a tip about this?<br /><br />Thanks in advance<br /><br
/>Adhemar<br /><br /></font></font></span></font>

[GUSDEV] change in loadresources

[Deborah P. <pi...@pc...>]

There has been a change in Loader.pm which is used by loadresources. 
Loader.pm now calls a script InsertUserProjectGroupFromGusConfig which 
adds the user, the project, and group to the relevant tables in core. It 
also makes rows in the core.userproject and core.usergroup table linking 
tables. It uses the information supplied in the user's gus.properties or 
gus.config file largely but needs a couple extra values noted below.  
There are a few important points that should be known:

1) The properties file used by loadresources should now have 3 
additional key/value pairs for:

firstName
lastName
projectRelease

These are values required by the script that are not in the gus 
properties(config) file.

2) The script won't duplicate userinfo rows if the users login is 
already found, nor will it add duplicates to the other tables.

3) The script can be run as a stand alone.

Please update GUS to get the changes incorporated into Loader.pm and the 
new script.

                                                                              

[GUSDEV] try using a resources pipeline

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

fabricio and all gus users-

the best way to run plugins is with a resources pipeline. attached=20
please find a sample resources.prop file and resources.xml file.

you use a resources XML file with the 'loadresources' command. the=20
purpose is to be able to start with an empty gus instance, as produced=20
by the gus installation, and then with one command (loadresources) to=20
fill the database up with all the datasets you need. (you don't need to=20
start with an empty gus, its just that the system is powerful enough to=20
be able to do so).

the resources pipeline works in conjunction with a "resources=20
repository." The repository lives in your file system (at a location you=20
specify). For each resource (eg, SequenceOntology) it stores:
- the files for the resource
- the version of the resource
- the wget arguments used to get the resource from its ftp site
- or, if the resource is gotten "manually", ie, not automatically from=20
an ftp site, the details of the contact info, etc

the resources repository acts as a resource cache. the first time you=20
request a resource from it, the repository gets the file(s) from the=20
external ftp site. when you request that same resource again (eg, SO=20
version 1.4), the respository just gives you the resource that it is=20
already holding.

here is what the resources pipeline does
1. initializes a resource repository, if you don't already have one
2. initializes a pipeline directory in which all the files for the=20
pipeline are stored.
3. if you are not already in GUS as a user (eg, Core.UserInfo), it=20
automatically adds you (this detail is coming later today)
4. for each resource that you specify in the resources XML file:
- inserts into the db the ExternalDatabase and ExternalDatabaseRelease=20
for that resource
- calls the resources repository to acquire the resource (the XML=20
provides the wget command to do so)
- places the resource in a downloads/ directory in the pipeline/ director=
y
- calls any pre-processing required to prepare the resource for use by=20
plugins (this is called "unpacking")
- automatically registers the plugin you will use to load the resource=20
(this detail is coming in a few days)
- calls the plugin to load the data
- sets a signal in the pipeline/ dir to state that this step has been=20
completed. this way, you can re-run the pipeline and resources that are=20
already loaded won't be loaded again; only those that are new will be

by using a pipeline like this, you have created a detailed re-runnable=20
and complete specification for how you load your data into gus. at CBIL,=20
this is the backbone of how we manage all our big projects. it requires=20
some additional work up front. but, once you have the resources.xml, you=20
can always easily recreate your database from scratch, and have a=20
permanant and accurate record of how the db was built.

once you have used the resources pipeline to load all the resources,=20
then you can use an analysis pipeline to do all the analysis. (how to do=20
that is not discussed here).

steve

Fabr=EDcio wrote:

>Ok Steve,
>
>I'm trying to load a genbank file. More specifically, this file:
>
>http://www.de9.ime.eb.br/~fabricio/tvivax.gb
>
>I will do the tests and then I will report to you my tries ok?
>
>Thanks very much,
>
>Fabr=EDcio.
>
>
>-----Mensagem original-----
>De: Steve Fischer [mailto:sfi...@pc...]=20
>Enviada em: quarta-feira, 14 de setembro de 2005 21:33
>Para: Fabr=EDcio
>Assunto: Re: RES: InsertSequenceFeatures
>
>fabricio-
>
>ok, get the latest GUS/Supported.
>
>the plugin has been tested enough that its ready for you. let me know=20
>what problems you have.
>
>what kind of data are you loading?
>
>steve
>
>Fabr=EDcio wrote:
>
> =20
>
>>Ok Steve,
>>
>>I recognize your tasks... I know how many busy you must be.
>>
>>Thanks again,
>>
>>Fabr=EDcio.=20
>>
>>-----Mensagem original-----
>>De: Steve Fischer [mailto:sfi...@pc...]=20
>>Enviada em: ter=E7a-feira, 13 de setembro de 2005 22:41
>>Para: Fabr=EDcio
>>Assunto: Re: InsertSequenceFeatures
>>
>>fabricio-
>>
>>we are in the active process of testing and debugging the plugin. i am=20
>>so sorry that you have to wait for this. i made much good progress in=20
>>the debugging, and, i would be doing more right now, but, today and muc=
h=20
>>of tomorrow we are moving our databases to our big new servers. so, i=20
>>won't be finished until a couple more days.
>>
>>the plugin is my highest priority (we desperately need it too!)
>>
>>i think you'll really like the plugin when i release it.
>>
>>sorry again!
>>
>>steve
>>
>>Fabr=EDcio wrote:
>>
>>=20
>>
>>   =20
>>
>>>Hello Steve,
>>>
>>>Some days ago, I tried to insert a genbank file to GUS using your=20
>>>plugin InsertSequenceFeatures.pm. For that moment I received an error=20
>>>saying this:
>>>
>>>Can't locate object method "geneNameIds" via package=20
>>>"GUS::Supported::Plugin::InsertSequenceFeatures" at=20
>>>$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line=
 920
>>>
>>>I saw in plugin that there is a method call to geneNameIds, but I=20
>>>didn=92t find this method definition as =93sub=94 inside=20
>>>InsertSequenceFeatures.pm.
>>>
>>>Is it a not yet implemented method? Or is it another kind of error?
>>>
>>>Thanks for your help,
>>>
>>>Fabr=EDcio
>>>
>>>  =20
>>>
>>>     =20
>>>
>>=20
>>
>>   =20
>>
>
>
> =20
>

Re: [GUSDEV] GUS 3.5 Plugins

[steve <sfi...@pc...>]

Adhemar-

the GBParser is no longer supported in gus 3.5.=20

We have a replacement plugin GUS::Supported::Plugin::InsertSequenceFeatur=
es.

It is being actively tested now.   The testing should be done this week.

I'll let all know when it is ready for general use, later this week.

Steve

Adhemar Zerlotini Neto wrote:

>
> Hi all,
>
> I'm trying to upload some genbank files and then run blast with this=20
> data against the NRDB I already loaded.
>
> I think the problem is that I haven't the right plugin to GUS 3.5=20
> version. I've got the following error using the GBParser plugin:
>
> ga GUS::Community::Plugin::GBParser
>
> Database version does not match required version for Plugin.
> Database Version: 3.5    Plugin Version: HASH(0x8f84b78)
>
> Issuing rollback() for database handle being DESTROY'd without=20
> explicit disconnect().
>
> How can I solve this?
>
> Thanks in advance
>
>
> Adhemar Zerlotini Neto
> Centro de Pesquisas Ren=E9 Rachou - FIOCRUZ
> Av. Augusto de Lima 1715
> BH MG 30190-002, Brazil
> Phone: +55-31-3349-7785=20
> ------------------------------------------------------- SF.Net email=20
> is Sponsored by the Better Software Conference & EXPO September 19-22,=20
> 2005 * San Francisco, CA * Development Lifecycle Practices Agile &=20
> Plan-Driven Development * Managing Projects & Teams * Testing & QA=20
> Security * Process Improvement & Measurement *=20
> http://www.sqe.com/bsce5sf=20
> _______________________________________________ Gusdev-gusdev mailing=20
> list Gus...@li...=20
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev=20

[GUSDEV] GUS 3.5 Plugins

[Adhemar Z. N. <ad...@cp...>]

<br />Hi all,<br /><br />I'm trying to upload some genbank files and then
run blast with this data against the NRDB I already loaded.<br /><br />I
think the problem is that I haven't the right plugin to GUS 3.5 version.
I've got the following error using the GBParser plugin:<br /><font
size=3D"2"><br style=3D"font-family: courier new,courier,monospace;" /><s=
pan
style=3D"font-family: courier new,courier,monospace;">ga
GUS::Community::Plugin::GBParser</span><br style=3D"font-family: courier
new,courier,monospace;" /><br style=3D"font-family: courier
new,courier,monospace;" /><span style=3D"font-family: courier
new,courier,monospace;">Database version does not match required version
for Plugin.</span><br style=3D"font-family: courier new,courier,monospace=
;"
/><span style=3D"font-family: courier new,courier,monospace;">Database
Version: 3.5=A0=A0=A0 Plugin Version: HASH(0x8f84b78)</span><br
style=3D"font-family: courier new,courier,monospace;" /><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">Issuing rollback() =
for
database handle being DESTROY'd without explicit
disconnect().</span></font><br /><br />How can I solve this?<br /><br
/>Thanks in advance<br /><br /><br />Adhemar Zerlotini Neto<br />Centro d=
e
Pesquisas Ren=E9 Rachou - FIOCRUZ<br />Av. Augusto de Lima 1715<br />BH M=
G
30190-002, Brazil<br />Phone: +55-31-3349-7785

Re: [GUSDEV] schema documentation and the plugins

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

josef-

thanks.  i think the problem you are having is demonstrating that ISF 
plugin is not fully tested.   We are still gearing up to use it for real 
in-house.   I released it as "beta" but, i think that is optimistic.    
The code to handle comments, i think, has not yet been exercised by our 
testing.  

but, it will very soon, as we have been spending the past few days 
unexpectedly getting straight where we are to get our P.falciparum 
chromosome files from.  

i think we've gotten that straight, so, at last will be running the 
plugin on that data, as further testing.

in your case, the code seems to be calling a method value() that is not 
supported by Bio::AnnotationI.   I'll probably fix it in the next couple 
of days.

thanks,
steve

Josef Jurek wrote:

>Often, it is difficult to understand the intended use of many
>of the schema tables and columns as the documentation on
>this is still incomplete.
>
>Recently, it struck me that many of the supported plugins are
>a sort of schema documentation by themselves and with that,
>I have been trying to run the recently discussed
>InsertSequenceFeatures plugin, though I have yet to be successful.
>I have been running this plugin with the following arguments:
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures \
>    --mapFile $HOME/xml/genbank2gus.xml \
>    --seqFile AT_chr5_T2I1.gbk \
>    --fileFormat genbank \
>    --soCvsVersion 1.42 \
>    --extDbName ncbi \
>    --extDbRlsVer genbank \
>    --sqlVerbose \
>    --commit
>
>and depending on the genbank file (I have tried several)
>the plugin bombs at one of two errors.  Either:
>
>   Can't locate object method "value" via package "Bio::Annotation::Comment" at
>     /home2/gus5/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 655,
>       <GEN14> line 77428.
>
>or
>
>   SQL ERROR!! involving
>   INSERT INTO DoTS.Keyword (  keyword, group_write, other_read, group_read, user_read,
>      row_user_id, other_write, modification_date, row_alg_invocation_id, row_project_id,
>      row_group_id, keyword_id, user_write )
>     VALUES   (  null, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>   Values: 1, 1, 1, 1, 1, 0, 88, 1, 1, 7, 1 at
>     /home2/gus5/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>
>where the plugin trys to insert a row into DoTS.Keyword leaving the
>column "keyword" NULL.
>
>
>Can someone just suggest a genbank file that is known to have
>worked with this plugin in the recent past?
>
>What of "Bio::Annotation::Comment" error?  Is this a known bug?
>
>On a related note; concerning the SRes.SequenceOntology table and
>the InsertSequenceOntology plugin, what is the difference between
>the columns so_version and so_cvs_version?
>
>Thank you for your insight.
>
>Josef
>
>
>
>Josef Jurek, Ph.D.
>
>Daphne Preuss Laboratory
>Molecular Genetics and Cell Biology
>The University of Chicago
>ju...@cs...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>
>
>
>
>-------------------------------------------------------
>SF.Net email is Sponsored by the Better Software Conference & EXPO
>September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
>Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
>Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[GUSDEV] schema documentation and the plugins

[Josef J. <ju...@cs...>]

Often, it is difficult to understand the intended use of many
of the schema tables and columns as the documentation on
this is still incomplete.

Recently, it struck me that many of the supported plugins are
a sort of schema documentation by themselves and with that,
I have been trying to run the recently discussed
InsertSequenceFeatures plugin, though I have yet to be successful.
I have been running this plugin with the following arguments:

 ga GUS::Supported::Plugin::InsertSequenceFeatures \
    --mapFile $HOME/xml/genbank2gus.xml \
    --seqFile AT_chr5_T2I1.gbk \
    --fileFormat genbank \
    --soCvsVersion 1.42 \
    --extDbName ncbi \
    --extDbRlsVer genbank \
    --sqlVerbose \
    --commit

and depending on the genbank file (I have tried several)
the plugin bombs at one of two errors.  Either:

   Can't locate object method "value" via package "Bio::Annotation::Comment" at
     /home2/gus5/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 655,
       <GEN14> line 77428.

or

   SQL ERROR!! involving
   INSERT INTO DoTS.Keyword (  keyword, group_write, other_read, group_read, user_read,
      row_user_id, other_write, modification_date, row_alg_invocation_id, row_project_id,
      row_group_id, keyword_id, user_write )
     VALUES   (  null, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
   Values: 1, 1, 1, 1, 1, 0, 88, 1, 1, 7, 1 at
     /home2/gus5/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166

where the plugin trys to insert a row into DoTS.Keyword leaving the
column "keyword" NULL.


Can someone just suggest a genbank file that is known to have
worked with this plugin in the recent past?

What of "Bio::Annotation::Comment" error?  Is this a known bug?

On a related note; concerning the SRes.SequenceOntology table and
the InsertSequenceOntology plugin, what is the difference between
the columns so_version and so_cvs_version?

Thank you for your insight.

Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [GUSDEV] synonym table(s)

[Michael S. <msa...@pc...>]

A possible 4th option, especially if the use of synonyms is expected to
grow:

We could use a soft linking table here that would allow *any* item in the
database to be tagged with a synonym.

There are some pros and cons with this approach, namely that it simplifies
the schema a bit, but queries (i.e. joining for synonyms) becomes more
complex.

--Mike


On 9/9/05 8:36 AM, "Deborah Pinney" <pi...@pc...> wrote:

> I would like to propose another table(s) to hold synonym information but
> I'm uncertain what to propose. Therefore, I would like to solicit opinions.
> 
> Immediate motivation:
> Genetic markers often have aliases and, as in many cases, there could be
> more than one alias per marker. Storing multiple aliases as a string
> list in a single attribute of a view or table is clumsy and results in
> inefficient queries. The obvious solution is a separate table for
> aliases which I've called synonyms.
> 
> There are several possible tables that could be proposed:
> 1) The proposed view to hold Genetic Markers is a view of NAFeatureImp
> so we could have a NAFeatureSynonym table with hard links to NAFeature.
> 2) We could have a GeneticMarkerSynonym table dedicated to a
> GeneticMarker view, which would also have hard links to NAFeature.
> 3) We could have a Synonym table with linking tables  - e.g.
> SynonymNAFeature - and the linking table could have hard links to
> Synonym and NAFeature.
> 
> There are others but these capture the general idea. I am partial to the
> third as this Synonym table could be multi-purpose while the linking
> tables could have only hard links.
> 
> Let me add, there are synonym tables in GUS -
> AAGeneSyynonym,GeneSynonym,ProteinSynonym,MoietySynonym,GOSynonym - but
> none that can be used for nafeatures.
> 
>                  
> Debbie
> 
> 
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev