gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] representing gene symbols

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

Steve Fischer wrote:

> folks-
> 1. introduce a GeneName table:
>   GeneName.gene_name_id
>   GeneName.name    --- the full name
>   GeneName.symbol  -- the symbol
>
> 2. introduce a GeneSynonym table:
>    GeneSynonym.gene_name_id     -- the GeneName it is a synonym for
>    GeneSynonym.name                  -- the full name of the synonym
>    GeneSynonym.symbol               -- the symbol
> these tables are treated as controlled vocabularies, downloaded from 
> sites such as HUGO and MGI.

Why do you want to separate the synonyms? It is implying that the 
GeneName table has an "approved" name and only one approved name, but 
approved by whom and what about alternate sources of information?  Also 
there should be a ExternalDatabaseRelease FK reference here. 
I would store all names in a single table and handle the 'approved' 
names either by a query to the ExternalDBRel (if you always prefer one 
authority to others) or in the GeneNameAssociation table with a bit column.

>
>
> 3. introduce a GeneNameAssociation table -- a mapping between Gene and 
> GeneName (better name for this??)
>   GeneNameAssociation.gene_id
>   GeneNameAssociation.gene_name_id
>   GeneNameAssociaction.review_status_id
>   GeneNameAssociaction.is_not 

 Why "is_not" ? Is this a hold-over from GO terms? I don't see how it 
applies to GeneName.


Angel

[Gusdev-gusdev] representing gene symbols

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

folks-

right now in GUS, we have a bunch of tables and attribute that relate to 
gene symbols, names and aliases:

Dots::Gene.name
Dots::Gene.gene_symbol
Dots::GeneAlias
Sres::DbRef.gene_symbol   (this is pretty clearly a hack.  DbRef is 
intended to store references to external database entries.  it is 
hackish to encode in the schema that we assume that such entries are 
gene records.  they could easily be proteins or journals, whatever)

This schema is being used by the DoTS project to hold both automated 
assignments of gene_symbol (Sres::DbRef) and manual assignments.  The 
problem for the DoTS project is that these disparate ways of making 
assignments are not managed as a coherent whole. The manual and 
automated assignments are not queried together.  

I am thinking that we should consider a different approach, one modeled 
on how we store GO assignments.  It seems that Gene symbols and GO terms 
are very similar.  they are both amenable to contolled vocabs, and are 
both assigned by automated and manual operations.  This pattern may 
apply to other types of annotation as well.


1. introduce a GeneName table:
   GeneName.gene_name_id
   GeneName.name    --- the full name
   GeneName.symbol  -- the symbol

2. introduce a GeneSynonym table:
    GeneSynonym.gene_name_id     -- the GeneName it is a synonym for
    GeneSynonym.name                  -- the full name of the synonym
    GeneSynonym.symbol               -- the symbol

these tables are treated as controlled vocabularies, downloaded from 
sites such as HUGO and MGI.


3. introduce a GeneNameAssociation table -- a mapping between Gene and 
GeneName (better name for this??)
   GeneNameAssociation.gene_id
   GeneNameAssociation.gene_name_id
   GeneNameAssociaction.review_status_id
   GeneNameAssociaction.is_not
   probably adopt here an instance and evidence mechanism similar to go 
assocation.

note that this implies a m-m relationship between gene and gene name. 
 while this might not be true in the ideal sense, it may well be true 
for tentative data, which is what we often have.  so, this model accepts 
that unfortunate fact, and does the best to preserve as much info as we can.

Re: [Gusdev-gusdev] Few ga plugins ..

[Dave B. <db...@pc...>]

These plugins are undergoing major revisions currently; the bottom two 
may even cease to exist!  

They are all related to our GO Prediction algorithm.  I will send mail 
when a new batch of fully tested and functional plugins for the algorithm 
are complete.

Dave


> >>CopyAASeqGoFuncToProtGoFunc     <-- I have latest copy of this
> >>DeleteGoPredictions             <-- I have latest copy of this
> >>MakeGoPredictions               <-- I have latest copy of this
> >>
> >>
> >>
> >>    
> >>
> >
> >
> >
> >-------------------------------------------------------
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> >  
> >
> 
> 
> 
> -------------------------------------------------------
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Re: [Gusdev-gusdev] Few ga plugins ..

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

so, chetna-  you have the latest CBIL.   also get the latest GUS from 
the sanger site and that should fix loadblastsimilaritiespk.

as indicated, the rest are under going gus 3.0 upgrades now.

steve

Deborah F. Pinney wrote:

>I used LoadBlastSimilaritiesPK within the last 5 days and the version I 
>used is in CVS. You will need to update it as well as two other modules, 
>GUS::Common::BulkSimilarity and CBIL::Util::A.
>
>InsertDbRefAndDbRefNASequence has not been tested yet so it may need some 
>work. It is scheduled for testing and use within the next week. I'll try 
>to remember to send e-mai when it is working and commited to CVS.
>
>The other three plugins are in the process of being updated and tested or 
>are obsolete. Dave Barkan can probably comment on those.
>
>                                               Deborah
>
>
>On Wed, 23 Apr 2003, Chetna D. Warade wrote:
>
>  
>
>>Hi,
>>
>>
>>I am attaching a document that includes 5 plugins which are either not 
>>able to compile or not find some module. Steve, I have downloaded CBIL 
>>tar version 3 and tested with the new tar too but still these scripts 
>>fail to compile.
>>
>>Following are the 5 plugins:
>>InsertDbRefAndDbRefNASequence   <--  I got newer version for this        
>>   
>>LoadBlastSimilaritiesPK         <-- I got newer version for this
>>CopyAASeqGoFuncToProtGoFunc     <-- I have latest copy of this
>>DeleteGoPredictions             <-- I have latest copy of this
>>MakeGoPredictions               <-- I have latest copy of this
>>
>>1) I get a feeling that problem could be an env variable or absence of 
>>some module. In InsertDbRefAndDbRefNASequence it is complaining about a 
>>package.
>>
>>2) The way I use these pluings for e.g. is:
>>
>>ga GUS::Common::Plugin::InsertDbRefAndDbRefNASequence --usage
>>or
>>ga GUS::GOPredict::Plugin::MakeGoPredictions --usage
>>
>>Just want to make sure that I use correct syntax.
>>
>>Hope to hear from you all,
>>Thanks,
>>Chetna
>>
>>
>>    
>>
>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
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>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] Few ga plugins ..

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

I used LoadBlastSimilaritiesPK within the last 5 days and the version I 
used is in CVS. You will need to update it as well as two other modules, 
GUS::Common::BulkSimilarity and CBIL::Util::A.

InsertDbRefAndDbRefNASequence has not been tested yet so it may need some 
work. It is scheduled for testing and use within the next week. I'll try 
to remember to send e-mai when it is working and commited to CVS.

The other three plugins are in the process of being updated and tested or 
are obsolete. Dave Barkan can probably comment on those.

                                               Deborah


On Wed, 23 Apr 2003, Chetna D. Warade wrote:

> Hi,
> 
> 
> I am attaching a document that includes 5 plugins which are either not 
> able to compile or not find some module. Steve, I have downloaded CBIL 
> tar version 3 and tested with the new tar too but still these scripts 
> fail to compile.
> 
> Following are the 5 plugins:
> InsertDbRefAndDbRefNASequence   <--  I got newer version for this        
>    
> LoadBlastSimilaritiesPK         <-- I got newer version for this
> CopyAASeqGoFuncToProtGoFunc     <-- I have latest copy of this
> DeleteGoPredictions             <-- I have latest copy of this
> MakeGoPredictions               <-- I have latest copy of this
> 
> 1) I get a feeling that problem could be an env variable or absence of 
> some module. In InsertDbRefAndDbRefNASequence it is complaining about a 
> package.
> 
> 2) The way I use these pluings for e.g. is:
> 
> ga GUS::Common::Plugin::InsertDbRefAndDbRefNASequence --usage
> or
> ga GUS::GOPredict::Plugin::MakeGoPredictions --usage
> 
> Just want to make sure that I use correct syntax.
> 
> Hope to hear from you all,
> Thanks,
> Chetna
> 
> 

[Gusdev-gusdev] Few ga plugins ..

[Chetna D. W. <ch...@ug...>]

Hi,


I am attaching a document that includes 5 plugins which are either not 
able to compile or not find some module. Steve, I have downloaded CBIL 
tar version 3 and tested with the new tar too but still these scripts 
fail to compile.

Following are the 5 plugins:
InsertDbRefAndDbRefNASequence   <--  I got newer version for this        
   
LoadBlastSimilaritiesPK         <-- I got newer version for this
CopyAASeqGoFuncToProtGoFunc     <-- I have latest copy of this
DeleteGoPredictions             <-- I have latest copy of this
MakeGoPredictions               <-- I have latest copy of this

1) I get a feeling that problem could be an env variable or absence of 
some module. In InsertDbRefAndDbRefNASequence it is complaining about a 
package.

2) The way I use these pluings for e.g. is:

ga GUS::Common::Plugin::InsertDbRefAndDbRefNASequence --usage
or
ga GUS::GOPredict::Plugin::MakeGoPredictions --usage

Just want to make sure that I use correct syntax.

Hope to hear from you all,
Thanks,
Chetna

Re: [Gusdev-gusdev] LoadGoOntology

[Chetna D. W. <ch...@ug...>]

Hi Steve,

1)
Here's the result:
[chetna@mango chetna]$ cd 
/home/projects/CBIL/Bio/lib/perl/GeneOntolgyParser/
[chetna@mango GeneOntolgyParser]$ ls 
ParseDemo.pm  Parser.pm  Store.pm  Term.pm
[chetna@mango GeneOntolgyParser]$ env | grep PROJECT_HOME
PROJECT_HOME=/home/projects
[chetna@mango GeneOntolgyParser]$ 

2) I downloaded CBIL_v1-2-0.tar on Mar 12th.

Thanks,
Chetna



---------Included Message----------
>Date: Fri, 18 Apr 2003 12:37:14 -0400
>From: "Steve Fischer" <st...@pc...>
>Cc: "Dave Barkan" <db...@pc...>, 
<gus...@li...>
>Subject: Re: [Gusdev-gusdev] LoadGoOntology
>
>chetna-
>
>which version of CBIL do you have?  (ie, which .tar file did you 
download?)
>
>can you do this, and send the results.
> ls $PROJECT_HOME/CBIL/Bio/lib/perl/GeneOntologyParser/
>
>steve
>
>Chetna D. Warade wrote:
>
>>Hi Dave,
>>
>>Thanks for looking into it. As Jonathan said in the previous email, he 

>>is right about the fact that LoadGoAssoc uses GeneAssocParser/Parser 
>>whereas LoadGoOntology uses GeneOntologyParser/Parser. 
>>
>>I really appreciate your help. Please do let me know when could I 
>>download the new release of CBIL project.
>>
>>Thanks,
>>Chetna
>>
>>---------Included Message----------
>>  
>>
>>>Date: Fri, 18 Apr 2003 10:51:11 -0400 (EDT)
>>>From: "Dave Barkan" <db...@pc...>
>>>To: "Chetna D. Warade" <ch...@ug...>
>>>Cc: <gus...@li...>
>>>Subject: Re: [Gusdev-gusdev] LoadGoOntology
>>>
>>>Hi Chetna,
>>>
>>>I'm not sure why it's failing on your particular run, but I think the 

>>>first thing to try is downloading a new release of the CBIL project.  

>>>    
>>>
>>The 
>>  
>>
>>>GeneOntologyParser has undergone some minor changes recently so it 
>>>definitely couldn't hurt.
>>>
>>>Before you do that, we should definitely create a new release.  I 
will 
>>>    
>>>
>>
>>  
>>
>>>talk to Steve about it and let you know when it is safe to proceed.
>>>
>>>Thanks,
>>>Dave
>>>
>>>
>>>On Thu, 17 Apr 2003, Chetna D. Warade wrote:
>>>
>>>    
>>>
>>>>Hi,
>>>>
>>>>I am trying to:
>>>>ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting 
>>>>      
>>>>
>>@INC 
>>  
>>
>>>>error whereas when I run:
>>>>ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
>>>>
>>>>Following is the error:
>>>>
>>>>[chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
>>>>--usage
>>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
>>>>
>>>>ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC 
>>>>      
>>>>
>>(@INC 
>>  
>>
>>>>contains: /home/gus_home/lib/perl /usr/lib/perl5/5.6.1/i386-linux 
>>>>/usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux 
>>>>/usr/lib/perl5/site_perl/5.6.1 
>>>>      
>>>>
>>/usr/lib/perl5/site_perl/5.6.0/i386-linux 
>>  
>>
>>>>/usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl 
>>>>/usr/lib/perl5/vendor_perl/5.6.1/i386-linux 
>>>>/usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at 
>>>>/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 

>>>>      
>>>>
>>3.
>>  
>>
>>>>BEGIN failed--compilation aborted at 
>>>>/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 

>>>>      
>>>>
>>3.
>>  
>>
>>>>Compilation failed in require at (eval 1) line 1.
>>>>
>>>>
>>>>--------------------------- STACK TRACE -------------------------
>>>>        
>>>>
>>>>      
>>>>
>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>
>>>    
>>>
>>>>'Can\'t locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC 
>>>>      
>>>>
>>(@IN...') 
>>  
>>
>>>>called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
>>>>      
>>>>
>>line 
>>  
>>
>>>>248
>>>>        
>>>>
>>>>      
>>>>
>>>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>>>    
>>>
>>
>>  
>>
>>>>'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 361
>>>>        
>>>>
>>>>      
>>>>
>>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>>>    
>>>
>>
>>  
>>
>>>>'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>>>>        
>>>>
>>>>      
>>>>
>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>>>    
>>>
>>
>>  
>>
>>>>'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>>>>        
>>>>
>>>>      
>>>>
>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>>>    
>>>
>>
>>  
>>
>>>>'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
>>>>
>>>>Both LoadGoAssoc and LoadGoOntology need 
>>>>CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would 
it 
>>>>      
>>>>
>>
>>  
>>
>>>>fail for one and run for other.
>>>>
>>>>Thanks and hope to hear from you'll,
>>>>Chetna
>>>>
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This sf.net email is sponsored by:ThinkGeek
>>>>Welcome to geek heaven.
>>>>http://thinkgeek.com/sf
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>      
>>>>
>>>    
>>>
>>---------End of Included Message----------
>>
>>
>>
>>
>>-------------------------------------------------------
>>This sf.net email is sponsored by:ThinkGeek
>>Welcome to geek heaven.
>>http://thinkgeek.com/sf
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>  
>>
>
>
>
---------End of Included Message----------

Re: [Gusdev-gusdev] LoadGoOntology

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

chetna-

which version of CBIL do you have?  (ie, which .tar file did you download?)

can you do this, and send the results.
 ls $PROJECT_HOME/CBIL/Bio/lib/perl/GeneOntologyParser/

steve

Chetna D. Warade wrote:

>Hi Dave,
>
>Thanks for looking into it. As Jonathan said in the previous email, he 
>is right about the fact that LoadGoAssoc uses GeneAssocParser/Parser 
>whereas LoadGoOntology uses GeneOntologyParser/Parser. 
>
>I really appreciate your help. Please do let me know when could I 
>download the new release of CBIL project.
>
>Thanks,
>Chetna
>
>---------Included Message----------
>  
>
>>Date: Fri, 18 Apr 2003 10:51:11 -0400 (EDT)
>>From: "Dave Barkan" <db...@pc...>
>>To: "Chetna D. Warade" <ch...@ug...>
>>Cc: <gus...@li...>
>>Subject: Re: [Gusdev-gusdev] LoadGoOntology
>>
>>Hi Chetna,
>>
>>I'm not sure why it's failing on your particular run, but I think the 
>>first thing to try is downloading a new release of the CBIL project.  
>>    
>>
>The 
>  
>
>>GeneOntologyParser has undergone some minor changes recently so it 
>>definitely couldn't hurt.
>>
>>Before you do that, we should definitely create a new release.  I will 
>>    
>>
>
>  
>
>>talk to Steve about it and let you know when it is safe to proceed.
>>
>>Thanks,
>>Dave
>>
>>
>>On Thu, 17 Apr 2003, Chetna D. Warade wrote:
>>
>>    
>>
>>>Hi,
>>>
>>>I am trying to:
>>>ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting 
>>>      
>>>
>@INC 
>  
>
>>>error whereas when I run:
>>>ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
>>>
>>>Following is the error:
>>>
>>>[chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
>>>--usage
>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
>>>
>>>ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC 
>>>      
>>>
>(@INC 
>  
>
>>>contains: /home/gus_home/lib/perl /usr/lib/perl5/5.6.1/i386-linux 
>>>/usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux 
>>>/usr/lib/perl5/site_perl/5.6.1 
>>>      
>>>
>/usr/lib/perl5/site_perl/5.6.0/i386-linux 
>  
>
>>>/usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl 
>>>/usr/lib/perl5/vendor_perl/5.6.1/i386-linux 
>>>/usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at 
>>>/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 
>>>      
>>>
>3.
>  
>
>>>BEGIN failed--compilation aborted at 
>>>/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 
>>>      
>>>
>3.
>  
>
>>>Compilation failed in require at (eval 1) line 1.
>>>
>>>
>>>--------------------------- STACK TRACE -------------------------
>>>        
>>>
>>>      
>>>
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>
>>    
>>
>>>'Can\'t locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC 
>>>      
>>>
>(@IN...') 
>  
>
>>>called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
>>>      
>>>
>line 
>  
>
>>>248
>>>        
>>>
>>>      
>>>
>>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
>>    
>>
>
>  
>
>>>'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 361
>>>        
>>>
>>>      
>>>
>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
>>    
>>
>
>  
>
>>>'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>>>        
>>>
>>>      
>>>
>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
>>    
>>
>
>  
>
>>>'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>>>        
>>>
>>>      
>>>
>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
>>    
>>
>
>  
>
>>>'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
>>>
>>>Both LoadGoAssoc and LoadGoOntology need 
>>>CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
>>>      
>>>
>
>  
>
>>>fail for one and run for other.
>>>
>>>Thanks and hope to hear from you'll,
>>>Chetna
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This sf.net email is sponsored by:ThinkGeek
>>>Welcome to geek heaven.
>>>http://thinkgeek.com/sf
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>      
>>>
>>    
>>
>---------End of Included Message----------
>
>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

Re: [Gusdev-gusdev] LoadGoOntology

[Chetna D. W. <ch...@ug...>]

Hi Dave,

Thanks for looking into it. As Jonathan said in the previous email, he 
is right about the fact that LoadGoAssoc uses GeneAssocParser/Parser 
whereas LoadGoOntology uses GeneOntologyParser/Parser. 

I really appreciate your help. Please do let me know when could I 
download the new release of CBIL project.

Thanks,
Chetna

---------Included Message----------
>Date: Fri, 18 Apr 2003 10:51:11 -0400 (EDT)
>From: "Dave Barkan" <db...@pc...>
>To: "Chetna D. Warade" <ch...@ug...>
>Cc: <gus...@li...>
>Subject: Re: [Gusdev-gusdev] LoadGoOntology
>
>Hi Chetna,
>
>I'm not sure why it's failing on your particular run, but I think the 
>first thing to try is downloading a new release of the CBIL project.  
The 
>GeneOntologyParser has undergone some minor changes recently so it 
>definitely couldn't hurt.
>
>Before you do that, we should definitely create a new release.  I will 

>talk to Steve about it and let you know when it is safe to proceed.
>
>Thanks,
>Dave
>
>
>On Thu, 17 Apr 2003, Chetna D. Warade wrote:
>
>> Hi,
>> 
>> I am trying to:
>> ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting 
@INC 
>> error whereas when I run:
>> ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
>> 
>> Following is the error:
>> 
>> [chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
>> --usage
>> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
>> 
>> ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC 
(@INC 
>> contains: /home/gus_home/lib/perl /usr/lib/perl5/5.6.1/i386-linux 
>> /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux 
>> /usr/lib/perl5/site_perl/5.6.1 
/usr/lib/perl5/site_perl/5.6.0/i386-linux 
>> /usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl 
>> /usr/lib/perl5/vendor_perl/5.6.1/i386-linux 
>> /usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at 
>> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 
3.
>> BEGIN failed--compilation aborted at 
>> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 
3.
>> Compilation failed in require at (eval 1) line 1.
>> 
>> 
>> --------------------------- STACK TRACE -------------------------
>>         
>>
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>
>> 'Can\'t locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC 
(@IN...') 
>> called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
line 
>> 248
>>         
>>
>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 361
>>         
>>
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>>         
>>
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
>> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>>         
>>
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 

>> 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
>> 
>> Both LoadGoAssoc and LoadGoOntology need 
>> CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 

>> fail for one and run for other.
>> 
>> Thanks and hope to hear from you'll,
>> Chetna
>> 
>> 
>> 
>> 
>> -------------------------------------------------------
>> This sf.net email is sponsored by:ThinkGeek
>> Welcome to geek heaven.
>> http://thinkgeek.com/sf
>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> 
>
>
---------End of Included Message----------

Re: [Gusdev-gusdev] LoadGoOntology

[Dave B. <db...@pc...>]

Hi Chetna,

I'm not sure why it's failing on your particular run, but I think the 
first thing to try is downloading a new release of the CBIL project.  The 
GeneOntologyParser has undergone some minor changes recently so it 
definitely couldn't hurt.

Before you do that, we should definitely create a new release.  I will 
talk to Steve about it and let you know when it is safe to proceed.

Thanks,
Dave


On Thu, 17 Apr 2003, Chetna D. Warade wrote:

> Hi,
> 
> I am trying to:
> ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting @INC 
> error whereas when I run:
> ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
> 
> Following is the error:
> 
> [chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
> --usage
> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> 
> ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@INC 
> contains: /home/gus_home/lib/perl /usr/lib/perl5/5.6.1/i386-linux 
> /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux 
> /usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl/5.6.0/i386-linux 
> /usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl 
> /usr/lib/perl5/vendor_perl/5.6.1/i386-linux 
> /usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at 
> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
> BEGIN failed--compilation aborted at 
> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
> Compilation failed in require at (eval 1) line 1.
> 
> 
> --------------------------- STACK TRACE -------------------------
>         
> GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'Can\'t locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@IN...') 
> called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
> 248
>         
> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 361
>         
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>         
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>         
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> 
> Both LoadGoAssoc and LoadGoOntology need 
> CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
> fail for one and run for other.
> 
> Thanks and hope to hear from you'll,
> Chetna
> 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] LoadGoOntology

[Jonathan C. <cra...@pc...>]

Hi Chetna-

Chetna D. Warade wrote:
> I am trying to:
> ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting @INC 
> error whereas when I run:
> ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
> 
> Following is the error:
> 
> [chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
> --usage
> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> 
> ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@INC 

I don't know the answer to this, but Dave Barkan has been working actively
on the GO-related plugins, and should be able to shed some light on the
problem.

> Both LoadGoAssoc and LoadGoOntology need 
> CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
> fail for one and run for other.

Are you sure about that?  I just checked what's currently in CVS and
while LoadGoOntology.pm does "use" CBIL::Bio::GeneOntologyParser::Parser,
it looks like LoadGoAssoc uses CBIL::Bio::GeneAssocParser::Parser instead,
which would account for the difference in behavior you're seeing.  Perhaps
you have to download a new version of the CBIL tar file (and perhaps we
first need to generate one!)

Jonathan

-- 
Jonathan Crabtree
Senior Programmer Analyst
CBIL, Center for Bioinformatics
University of Pennsylvania, Philadelphia, PA

[Gusdev-gusdev] LoadGoOntology

[Chetna D. W. <ch...@ug...>]

Hi,

I am trying to:
ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting @INC 
error whereas when I run:
ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!

Following is the error:

[chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
--usage
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop

ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@INC 
contains: /home/gus_home/lib/perl /usr/lib/perl5/5.6.1/i386-linux 
/usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux 
/usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl/5.6.0/i386-linux 
/usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl 
/usr/lib/perl5/vendor_perl/5.6.1/i386-linux 
/usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at 
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
BEGIN failed--compilation aborted at 
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
Compilation failed in require at (eval 1) line 1.


--------------------------- STACK TRACE -------------------------
        
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'Can\'t locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@IN...') 
called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
248
        
GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'GUS::GOPredict::Plugin::LoadGoOntology') called at 
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 361
        
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'GUS::GOPredict::Plugin::LoadGoOntology') called at 
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
        
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'GUS::GOPredict::Plugin::LoadGoOntology') called at 
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
        
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11

Both LoadGoAssoc and LoadGoOntology need 
CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
fail for one and run for other.

Thanks and hope to hear from you'll,
Chetna

[Gusdev-gusdev] how do i get a gene's taxon?

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

i want to open up the following for discussion:  
  - currently (3.0), if given a gene id, how does one get the gene's 
taxon?  as a slightly naive user of the schema, i confess that i am 
stumped by this (and assumed it would be straightforward)
  - should this be a direct attribute of the gene (and, any answer we 
give here might apply in parallel to RNA)?

steve

Re: [Gusdev-gusdev] loadtaxon

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

You need to get the taxonomy files from NCBI which can be obtained from
their ftp site: ftp://ftp.ncbi.nih.gov/pub/taxonomy/

The file you need to load these tables (Taxon,TaxonName, and GeneticCode)
can be found there: taxdump.tar.gz

You will need to tar the file before running the plug-in and put the
options, --node, --name, --gencode, with the corresponding full path and
name of the corresponding files on the command line. The plugin should
fill all three tables.

                                                      Debbie


On Sat, 29 Mar 2003, Chetna Warade wrote:

> Hi,
>
> I am running following:
>
> [chetna@mango chetna]$ ga GUS::Common::Plugin::LoadTaxon
> --gencode=/home/gusdev/gus3.0-checkouts/ncbi-taxonomy/gc.prt --commit
> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> Reading properties from /home/chetna/.gus.properties
> Provide the names of the names.dmp, nodes.dmp, and gencode.dmp files on
> the command line: !
> [chetna@mango chetna]$
>
> Now that I look into the table sres.geneticcode its empty. Same is the
> case with nodes.dmp and names.dmp
>
> Is there a sequence of actions to be done before running LoadTaxon?
>
> Thanks
> chetna
>
>
>
>
> -------------------------------------------------------
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>

[Gusdev-gusdev] loadtaxon

[Chetna W. <ch...@ar...>]

Hi,

I am running following:

[chetna@mango chetna]$ ga GUS::Common::Plugin::LoadTaxon
--gencode=/home/gusdev/gus3.0-checkouts/ncbi-taxonomy/gc.prt --commit
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/chetna/.gus.properties
Provide the names of the names.dmp, nodes.dmp, and gencode.dmp files on
the command line: !
[chetna@mango chetna]$

Now that I look into the table sres.geneticcode its empty. Same is the
case with nodes.dmp and names.dmp

Is there a sequence of actions to be done before running LoadTaxon? 

Thanks
chetna

Re: [Gusdev-gusdev] loadtaxon

[Jonathan C. <cra...@pc...>]

Chetna-

I don't have much experience with the new Perl object layer yet, but
perhaps the LoadTaxon plugin hasn't been updated to the new system?
Either that or maybe there's a small controlled vocabulary table of
parameter types that needs to be populated in the database (I think
there was some e-mail traffic to this effect fairly recently.)

Jonathan

[Gusdev-gusdev] loadtaxon

[Chetna W. <ch...@ar...>]

Hi guys,

I havent seen this error on the mailing list hence writing to you all. I
am getting following sequence of errors:

1) [chetna@mango chetna]$ ga GUS::Common::Plugin::LoadTaxon
--gencode=/home/gusdev/gus3.0-checkouts/ncbi-taxonomy/gc.prt --verbose
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/chetna/.gus.properties


prepareAndExecute:     SELECT *
      FROM Core.AlgorithmImplementation
     WHERE executable = 'GUS::Common::Plugin::LoadTaxon'
       AND cvs_revision    = '1.24'

prepareAndExecute: select * from core.algorithmimplementation where
executable = 'GUS::Common::Plugin::LoadTaxon'

USER ERROR: GUS::Common::Plugin::LoadTaxon has never been registered.
Please use 'ga +create GUS::Common::Plugin::LoadTaxon --commit'
Issuing rollback() for database handle being DESTROY'd without explicit
disconnect().

2) ----------------------
[chetna@mango chetna]$ ga +create GUS::Common::Plugin::LoadTaxon --commit
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/chetna/.gus.properties
'string' is not a legal param type for option gencode.
'boolean' is not a legal param type for option commit.
'string' is not a legal param type for option group.
'integer' is not a legal param type for option algoinvo.
'string' is not a legal param type for option user.
'string' is not a legal param type for option comment.
'string' is not a legal param type for option nodes.
'string' is not a legal param type for option gusconfigfile.
'string' is not a legal param type for option names.
'int' is not a legal param type for option restart.
'string' is not a legal param type for option project.

Hope to hearing from you
Chetna

Re: [Gusdev-gusdev] how finite are primary keys?

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

steve fischer wrote:
> jonathan-
> 
> i few people have recently asked me a question that you can best answer.
> 
> what if any is the limit to the size of primary keys?
> 
> this question comes out of the observation that we are burning through 
> primary keys when we test in non-commit mode.
> 
> i have been assuming that the limit is large enough that we don't need 
> to worry about exhausting them.
> 
> steve

Steve,

I asked one of our DBAs (Andy) and he replied with;

"It's limited by the datatype of the column it's on which, in the case of
GUS, is NUMBER(10) typically.  So, it will reach 9,999,999,999 and then
fall over.  The GO schema tables look similar.  In GUS I can see an
occasional composite primary key where one of the columns is NUMBER(6)
(eg. AASEQUENCEKEYWORDVER), so the limit would be six digits in that case."

Hope that helps.

Paul.

[Gusdev-gusdev] how finite are primary keys?

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

jonathan-

i few people have recently asked me a question that you can best answer.

what if any is the limit to the size of primary keys?

this question comes out of the observation that we are burning through 
primary keys when we test in non-commit mode.

i have been assuming that the limit is large enough that we don't need 
to worry about exhausting them.

steve

Re: [Gusdev-gusdev] Setting up your initial Users, etc

[Chetna W. <ch...@ar...>]

Hi Steve,

Thanks for the mail.

I am done with the ga +meta --commit. I am attaching the document that I
prepared for solving this problem.

Thanks
Chetna

> can you send your .gus.properties file?
> 
> thanks,
> steve
> 
> Chetna Warade wrote:
> 
> >Hi Steve,
> >
> >Thanks for the mail. As you said I changed userLogin == login of
> >core.userinfo so the error msg "ORA-01400: cannot insert NULL into
> >("CORE"."ALGORITHM"."ROW_USER_ID")" is gone. But now 
> >
> >DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> >("CORE"."ALGORITHM"."ROW_GROUP_ID") (DBD ERROR: OCIStmtExecute) at
> >/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 138.
> >
> >is coming. I verified that core.groupinfo has "ctegd" as name and "2" as
> >its group_id but I am wondering  why's the ga getting null value
> >
> >Hope to hear from you
> >chetna
> >
> >  
> >
> >>userName from gus.properties corresponds to the login attribute of 
> >>core.userinfo.
> >>
> >>i know this is confusing (we have known about this but didn't get to 
> >>fixing it)
> >>
> >>i think that we should consider renaming the property in .gus.property to:
> >>  userLogin=sfischer
> >>
> >>the databaseLogin is something like this:
> >>  databaseLogin=GUSrw
> >>
> >>meanwhile, i plan on improving the error message ga puts out in this 
> >>case so that it won't be hard to figure out what is going on.
> >>
> >>steve
> >>
> >>Chetna Warade wrote:
> >>
> >>    
> >>
> >>>Hi Dave,
> >>>
> >>>Yes I knew from gus 2.0 that the user in gus properties correspond to the
> >>>oracle user login. Is this true in gus 3.0 too - meaning databaseLogin in 
> >>>.gus.properties correspond to user_id in the core.userinfo. And is
> >>>userName any important (I did make the FIRST_NAME in Core.userinfo equal
> >>>to the $USER of .gus.properties).
> >>>
> >>>Thanks
> >>>Chetna
> >>>
> >>> 
> >>>
> >>>      
> >>>
> >>>>Forgot to mention this the first time; is the user you added in
> >>>>Core.UserInfo the same as the one in your .gus.properties file?
> >>>>
> >>>>If it is, then sorry, that's probably the extent of my usefulness in
> >>>>solving this problem!
> >>>>
> >>>>dave
> >>>>
> >>>>On Fri, 14 Mar 2003, Chetna Warade wrote:
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>>>>Hi guys,
> >>>>>
> >>>>>Yes I added a user in Core.UserInfo and Sres.Contact, but I still getting
> >>>>>the same error for ga +meta --commit. Can anyone tell me what tables I
> >>>>>need for projects and groups, Are they Core.GroupInfo and
> >>>>>Core.ProjectInfo?. In the meantime I am adding rows in these two tables
> >>>>>but please let me know if there are other table dependencies.
> >>>>>
> >>>>>Thanks to all for the help
> >>>>>Chetna
> >>>>>
> >>>>>
> >>>>>     
> >>>>>
> >>>>>          
> >>>>>
> >>>>>>yes, i agree.  chetna- you need to set up your Users and Projects, etc.
> >>>>>>Have you ever done this before?
> >>>>>>
> >>>>>>Jonathan Crabtree is away until Wed.  I don't know if he has set up
> >>>>>>scripts to assist in this process.  but, we should provide something to
> >>>>>>make this painless.
> >>>>>>
> >>>>>>I personally don't know the details of what is involved.
> >>>>>>
> >>>>>>Can anybody at PSU sketch what chetna should do?
> >>>>>>
> >>>>>>thanks
> >>>>>>steve
> >>>>>>
> >>>>>>Dave Barkan wrote:
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>            
> >>>>>>
> >>>>>>>Hi Chetna and all,
> >>>>>>>
> >>>>>>>I had this problem too at one point.  Someone needs to insert Chetna into
> >>>>>>>our UserInfo table as a user and give her the appropriate permissions.
> >>>>>>>
> >>>>>>>Dave
> >>>>>>>
> >>>>>>>On Fri, 14 Mar 2003, Chetna Warade wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>              
> >>>>>>>
> >>>>>>>>Hi Steve,
> >>>>>>>>
> >>>>>>>>I got the latest tars today morning, but I am getting:
> >>>>>>>>
> >>>>>>>>[chetna@mango install]$ ga +meta --commit
> >>>>>>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> >>>>>>>>Reading properties from /home/chetna/.gus.properties
> >>>>>>>><Core::Algorithm>
> >>>>>>>>  <name>GA-Plugin</name>
> >>>>>>>>  <description>GUS application framework for plugins</description>
> >>>>>>>>  <Core::AlgorithmImplementation>
> >>>>>>>>    <cvs_revision>1.36</cvs_revision>
> >>>>>>>>    <cvs_tag> </cvs_tag>
> >>>>>>>>    <executable>GUS::PluginMgr::GusApplication</executable>
> >>>>>>>>    <executable_md5>5947e17c4e9fea1d750cb5d9aaeee1db</executable_md5>
> >>>>>>>>    <description>update for GUS 3.0</description>
> >>>>>>>>    <Core::AlgorithmInvocation>
> >>>>>>>>      <start_time>sysdate</start_time>
> >>>>>>>>      <end_time>sysdate</end_time>
> >>>>>>>>      <machine_id>0</machine_id>
> >>>>>>>>      <cpus_used>1</cpus_used>
> >>>>>>>>      <result>meta</result>
> >>>>>>>>    </Core::AlgorithmInvocation>
> >>>>>>>>  </Core::AlgorithmImplementation>
> >>>>>>>></Core::Algorithm>
> >>>>>>>>DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> >>>>>>>>("CORE"."ALGORITHM"."ROW_USER_ID") (DBD ERROR: OCIStmtExecute) at
> >>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 138.
> >>>>>>>>
> >>>>>>>>SQL ERROR!! involving
> >>>>>>>>
> >>>>>>>>  INSERT INTO Core.Algorithm (  description, other_read, user_write,
> >>>>>>>>group_write, name, modification_date, user_read, algorithm_id,
> >>>>>>>>row_alg_invocation_id, group_read, other_write )
> >>>>>>>>  VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >>>>>>>>Values: GUS application framework for plugins, 1, 1, 1, GA-Plugin, 1, 45,
> >>>>>>>>1, 1, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 178
> >>>>>>>>
> >>>>>>>>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x84ee5e8)',
> >>>>>>>>'^J SQL ERROR!! involving^J ^J    INSERT INTO Core.Algorithm (  desc...')
> >>>>>>>>called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 141
> >>>>>>>>
> >>>>>>>>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x84ee5e8)',
> >>>>>>>>'GUS::ObjRelP::DbiDbHandle::st=HASH(0x86b7f10)', 'ARRAY(0x86b7f64)', '^J
> >>>>>>>>INSERT INTO Core.Algorithm (  description, other_read, user...') called at
> >>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 694
> >>>>>>>>
> >>>>>>>>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::Algorithm=HASH(0x84ee42c)',
> >>>>>>>>'GUS::Model::Core::Algorithm', 'HASH(0x85f7aa0)') called at
> >>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 641
> >>>>>>>>
> >>>>>>>>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::Algorithm=HASH(0x84ee42c)')
> >>>>>>>>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >>>>>>>>
> >>>>>>>>GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x84ee42c)')
> >>>>>>>>called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 339
> >>>>>>>>
> >>>>>>>>GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>>>>>undef) called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>>>>>line 283
> >>>>>>>>
> >>>>>>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>>>>>undef) called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>>>>>line 192
> >>>>>>>>
> >>>>>>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>>>>>'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> >>>>>>>>[chetna@mango install]$
> >>>>>>>>
> >>>>>>>>Thanks,
> >>>>>>>>Chetna
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>           
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>
> >>>>>>>>>can you get the install.tar and the gus.tar files again from cvsweb at
> >>>>>>>>>sanger.
> >>>>>>>>>
> >>>>>>>>>we have fixed an important problem that was introduced in the last few
> >>>>>>>>>days, and i think that will fix your problem.
> >>>>>>>>>
> >>>>>>>>>i just tested ga +meta --commit here and it seemed fine.
> >>>>>>>>>
> >>>>>>>>>steve
> >>>>>>>>>
> >>>>>>>>>Chetna Warade wrote:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>             
> >>>>>>>>>
> >>>>>>>>>                  
> >>>>>>>>>
> >>>>>>>>>>Hi Steve,
> >>>>>>>>>>
> >>>>>>>>>>Thanks for the mail.
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>               
> >>>>>>>>>>
> >>>>>>>>>>                    
> >>>>>>>>>>
> >>>>>>>>>>>1) can you send me the lines that you commented, so i can fix the problem.
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>                 
> >>>>>>>>>>>
> >>>>>>>>>>>                      
> >>>>>>>>>>>
> >>>>>>>>>>$GUS_HOME/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> >>>>>>>>>>line # 148
> >>>>>>>>>>line # 469
> >>>>>>>>>>line # 478
> >>>>>>>>>>Basically wherever string BIG (Actually BIGRBS1 in gus 3.0) appears.
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>               
> >>>>>>>>>>
> >>>>>>>>>>                    
> >>>>>>>>>>
> >>>>>>>>>>>2) the problem is that the tarball is excluding empty directories.  for
> >>>>>>>>>>>now, create the following directories:
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>                 
> >>>>>>>>>>>
> >>>>>>>>>>>                      
> >>>>>>>>>>>
> >>>>>>>>>>Thanks build is working correct now. But here's what I get:
> >>>>>>>>>>
> >>>>>>>>>>[chetna@mango chetna]$ ga +meta --commit
> >>>>>>>>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> >>>>>>>>>>Reading properties from /home/chetna/.gus.properties
> >>>>>>>>>><Core::Algorithm>
> >>>>>>>>>> <name>GA-Plugin</name>
> >>>>>>>>>> <description>GUS application framework for plugins</description>
> >>>>>>>>>> <Core::AlgorithmImplementation>
> >>>>>>>>>>   <cvs_revision>1.33</cvs_revision>
> >>>>>>>>>>   <cvs_tag> </cvs_tag>
> >>>>>>>>>>   <executable>GUS::PluginMgr::GusApplication</executable>
> >>>>>>>>>>   <executable_md5>0f9925c1794c069d858378c052a9d747</executable_md5>
> >>>>>>>>>>   <description>update for GUS 3.0</description>
> >>>>>>>>>>   <Core::AlgorithmInvocation>
> >>>>>>>>>>     <start_time>sysdate</start_time>
> >>>>>>>>>>     <end_time>sysdate</end_time>
> >>>>>>>>>>     <machine_id>0</machine_id>
> >>>>>>>>>>     <cpus_used>1</cpus_used>
> >>>>>>>>>>     <result>meta</result>
> >>>>>>>>>>   </Core::AlgorithmInvocation>
> >>>>>>>>>> </Core::AlgorithmImplementation>
> >>>>>>>>>></Core::Algorithm>
> >>>>>>>>>>DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> >>>>>>>>>>("CORE"."ALGORITHM"."ROW_USER_ID") (DBD ERROR: OCIStmtExecute) at
> >>>>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 137.
> >>>>>>>>>>
> >>>>>>>>>>SQL ERROR!! involving
> >>>>>>>>>>
> >>>>>>>>>> INSERT INTO Core.Algorithm (  description, other_read, user_write,
> >>>>>>>>>>group_write, name, modification_date, user_read, algorithm_id,
> >>>>>>>>>>row_alg_invocation_id, group_read, other_write )
> >>>>>>>>>> VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >>>>>>>>>>Values: GUS application framework for plugins, 1, 1, 1, GA-Plugin, 1, 23,
> >>>>>>>>>>1, 1, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 177.
> >>>>>>>>>>[chetna@mango chetna]$
> >>>>>>>>>>
> >>>>>>>>>>Hope to hear from you
> >>>>>>>>>>Chetna
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>               
> >>>>>>>>>>
> >>>>>>>>>>                    
> >>>>>>>>>>
> >>>>>>>>>             
> >>>>>>>>>
> >>>>>>>>>                  
> >>>>>>>>>
> >>>>>>>>-------------------------------------------------------
> >>>>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>>>>>>Get cracking and register here for some mind boggling fun and
> >>>>>>>>the chance of winning an Apple iPod:
> >>>>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>>>>>_______________________________________________
> >>>>>>>>Gusdev-gusdev mailing list
> >>>>>>>>Gus...@li...
> >>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>           
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>
> >>>>>>>-------------------------------------------------------
> >>>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>>>>>Get cracking and register here for some mind boggling fun and
> >>>>>>>the chance of winning an Apple iPod:
> >>>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>>>>_______________________________________________
> >>>>>>>Gusdev-gusdev mailing list
> >>>>>>>Gus...@li...
> >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>              
> >>>>>>>
> >>>>>>-------------------------------------------------------
> >>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>>>>Get cracking and register here for some mind boggling fun and
> >>>>>>the chance of winning an Apple iPod:
> >>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>>>_______________________________________________
> >>>>>>Gusdev-gusdev mailing list
> >>>>>>Gus...@li...
> >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>            
> >>>>>>
> >>>>>-------------------------------------------------------
> >>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>>>Get cracking and register here for some mind boggling fun and
> >>>>>the chance of winning an Apple iPod:
> >>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>>_______________________________________________
> >>>>>Gusdev-gusdev mailing list
> >>>>>Gus...@li...
> >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>
> >>>>>     
> >>>>>
> >>>>>          
> >>>>>
> >>>>-------------------------------------------------------
> >>>>This SF.net email is sponsored by:Crypto Challenge is now open! 
> >>>>Get cracking and register here for some mind boggling fun and 
> >>>>the chance of winning an Apple iPod:
> >>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>> 
> >>>
> >>>      
> >>>
> >>    
> >>
> >
> >
> >  
> >
> 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] Setting up your initial Users, etc

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

chetna-

can you send your .gus.properties file?

thanks,
steve

Chetna Warade wrote:

>Hi Steve,
>
>Thanks for the mail. As you said I changed userLogin == login of
>core.userinfo so the error msg "ORA-01400: cannot insert NULL into
>("CORE"."ALGORITHM"."ROW_USER_ID")" is gone. But now 
>
>DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
>("CORE"."ALGORITHM"."ROW_GROUP_ID") (DBD ERROR: OCIStmtExecute) at
>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 138.
>
>is coming. I verified that core.groupinfo has "ctegd" as name and "2" as
>its group_id but I am wondering  why's the ga getting null value
>
>Hope to hear from you
>chetna
>
>  
>
>>userName from gus.properties corresponds to the login attribute of 
>>core.userinfo.
>>
>>i know this is confusing (we have known about this but didn't get to 
>>fixing it)
>>
>>i think that we should consider renaming the property in .gus.property to:
>>  userLogin=sfischer
>>
>>the databaseLogin is something like this:
>>  databaseLogin=GUSrw
>>
>>meanwhile, i plan on improving the error message ga puts out in this 
>>case so that it won't be hard to figure out what is going on.
>>
>>steve
>>
>>Chetna Warade wrote:
>>
>>    
>>
>>>Hi Dave,
>>>
>>>Yes I knew from gus 2.0 that the user in gus properties correspond to the
>>>oracle user login. Is this true in gus 3.0 too - meaning databaseLogin in 
>>>.gus.properties correspond to user_id in the core.userinfo. And is
>>>userName any important (I did make the FIRST_NAME in Core.userinfo equal
>>>to the $USER of .gus.properties).
>>>
>>>Thanks
>>>Chetna
>>>
>>> 
>>>
>>>      
>>>
>>>>Forgot to mention this the first time; is the user you added in
>>>>Core.UserInfo the same as the one in your .gus.properties file?
>>>>
>>>>If it is, then sorry, that's probably the extent of my usefulness in
>>>>solving this problem!
>>>>
>>>>dave
>>>>
>>>>On Fri, 14 Mar 2003, Chetna Warade wrote:
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>>>Hi guys,
>>>>>
>>>>>Yes I added a user in Core.UserInfo and Sres.Contact, but I still getting
>>>>>the same error for ga +meta --commit. Can anyone tell me what tables I
>>>>>need for projects and groups, Are they Core.GroupInfo and
>>>>>Core.ProjectInfo?. In the meantime I am adding rows in these two tables
>>>>>but please let me know if there are other table dependencies.
>>>>>
>>>>>Thanks to all for the help
>>>>>Chetna
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>>>yes, i agree.  chetna- you need to set up your Users and Projects, etc.
>>>>>>Have you ever done this before?
>>>>>>
>>>>>>Jonathan Crabtree is away until Wed.  I don't know if he has set up
>>>>>>scripts to assist in this process.  but, we should provide something to
>>>>>>make this painless.
>>>>>>
>>>>>>I personally don't know the details of what is involved.
>>>>>>
>>>>>>Can anybody at PSU sketch what chetna should do?
>>>>>>
>>>>>>thanks
>>>>>>steve
>>>>>>
>>>>>>Dave Barkan wrote:
>>>>>>
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>Hi Chetna and all,
>>>>>>>
>>>>>>>I had this problem too at one point.  Someone needs to insert Chetna into
>>>>>>>our UserInfo table as a user and give her the appropriate permissions.
>>>>>>>
>>>>>>>Dave
>>>>>>>
>>>>>>>On Fri, 14 Mar 2003, Chetna Warade wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>         
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>>>Hi Steve,
>>>>>>>>
>>>>>>>>I got the latest tars today morning, but I am getting:
>>>>>>>>
>>>>>>>>[chetna@mango install]$ ga +meta --commit
>>>>>>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
>>>>>>>>Reading properties from /home/chetna/.gus.properties
>>>>>>>><Core::Algorithm>
>>>>>>>>  <name>GA-Plugin</name>
>>>>>>>>  <description>GUS application framework for plugins</description>
>>>>>>>>  <Core::AlgorithmImplementation>
>>>>>>>>    <cvs_revision>1.36</cvs_revision>
>>>>>>>>    <cvs_tag> </cvs_tag>
>>>>>>>>    <executable>GUS::PluginMgr::GusApplication</executable>
>>>>>>>>    <executable_md5>5947e17c4e9fea1d750cb5d9aaeee1db</executable_md5>
>>>>>>>>    <description>update for GUS 3.0</description>
>>>>>>>>    <Core::AlgorithmInvocation>
>>>>>>>>      <start_time>sysdate</start_time>
>>>>>>>>      <end_time>sysdate</end_time>
>>>>>>>>      <machine_id>0</machine_id>
>>>>>>>>      <cpus_used>1</cpus_used>
>>>>>>>>      <result>meta</result>
>>>>>>>>    </Core::AlgorithmInvocation>
>>>>>>>>  </Core::AlgorithmImplementation>
>>>>>>>></Core::Algorithm>
>>>>>>>>DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
>>>>>>>>("CORE"."ALGORITHM"."ROW_USER_ID") (DBD ERROR: OCIStmtExecute) at
>>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 138.
>>>>>>>>
>>>>>>>>SQL ERROR!! involving
>>>>>>>>
>>>>>>>>  INSERT INTO Core.Algorithm (  description, other_read, user_write,
>>>>>>>>group_write, name, modification_date, user_read, algorithm_id,
>>>>>>>>row_alg_invocation_id, group_read, other_write )
>>>>>>>>  VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>>>>>>>>Values: GUS application framework for plugins, 1, 1, 1, GA-Plugin, 1, 45,
>>>>>>>>1, 1, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 178
>>>>>>>>
>>>>>>>>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x84ee5e8)',
>>>>>>>>'^J SQL ERROR!! involving^J ^J    INSERT INTO Core.Algorithm (  desc...')
>>>>>>>>called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 141
>>>>>>>>
>>>>>>>>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x84ee5e8)',
>>>>>>>>'GUS::ObjRelP::DbiDbHandle::st=HASH(0x86b7f10)', 'ARRAY(0x86b7f64)', '^J
>>>>>>>>INSERT INTO Core.Algorithm (  description, other_read, user...') called at
>>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 694
>>>>>>>>
>>>>>>>>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::Algorithm=HASH(0x84ee42c)',
>>>>>>>>'GUS::Model::Core::Algorithm', 'HASH(0x85f7aa0)') called at
>>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 641
>>>>>>>>
>>>>>>>>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::Algorithm=HASH(0x84ee42c)')
>>>>>>>>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>>>>>>>>
>>>>>>>>GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x84ee42c)')
>>>>>>>>called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 339
>>>>>>>>
>>>>>>>>GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>>>>>undef) called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>>>>>line 283
>>>>>>>>
>>>>>>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>>>>>undef) called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>>>>>line 192
>>>>>>>>
>>>>>>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>>>>>'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
>>>>>>>>[chetna@mango install]$
>>>>>>>>
>>>>>>>>Thanks,
>>>>>>>>Chetna
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>           
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>>>>can you get the install.tar and the gus.tar files again from cvsweb at
>>>>>>>>>sanger.
>>>>>>>>>
>>>>>>>>>we have fixed an important problem that was introduced in the last few
>>>>>>>>>days, and i think that will fix your problem.
>>>>>>>>>
>>>>>>>>>i just tested ga +meta --commit here and it seemed fine.
>>>>>>>>>
>>>>>>>>>steve
>>>>>>>>>
>>>>>>>>>Chetna Warade wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>             
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>>>Hi Steve,
>>>>>>>>>>
>>>>>>>>>>Thanks for the mail.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>               
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>>>
>>>>>>>>>>>1) can you send me the lines that you commented, so i can fix the problem.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>
>>>>>>>>>>>                      
>>>>>>>>>>>
>>>>>>>>>>$GUS_HOME/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>>>>>>>>>>line # 148
>>>>>>>>>>line # 469
>>>>>>>>>>line # 478
>>>>>>>>>>Basically wherever string BIG (Actually BIGRBS1 in gus 3.0) appears.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>               
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>>>
>>>>>>>>>>>2) the problem is that the tarball is excluding empty directories.  for
>>>>>>>>>>>now, create the following directories:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>
>>>>>>>>>>>                      
>>>>>>>>>>>
>>>>>>>>>>Thanks build is working correct now. But here's what I get:
>>>>>>>>>>
>>>>>>>>>>[chetna@mango chetna]$ ga +meta --commit
>>>>>>>>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
>>>>>>>>>>Reading properties from /home/chetna/.gus.properties
>>>>>>>>>><Core::Algorithm>
>>>>>>>>>> <name>GA-Plugin</name>
>>>>>>>>>> <description>GUS application framework for plugins</description>
>>>>>>>>>> <Core::AlgorithmImplementation>
>>>>>>>>>>   <cvs_revision>1.33</cvs_revision>
>>>>>>>>>>   <cvs_tag> </cvs_tag>
>>>>>>>>>>   <executable>GUS::PluginMgr::GusApplication</executable>
>>>>>>>>>>   <executable_md5>0f9925c1794c069d858378c052a9d747</executable_md5>
>>>>>>>>>>   <description>update for GUS 3.0</description>
>>>>>>>>>>   <Core::AlgorithmInvocation>
>>>>>>>>>>     <start_time>sysdate</start_time>
>>>>>>>>>>     <end_time>sysdate</end_time>
>>>>>>>>>>     <machine_id>0</machine_id>
>>>>>>>>>>     <cpus_used>1</cpus_used>
>>>>>>>>>>     <result>meta</result>
>>>>>>>>>>   </Core::AlgorithmInvocation>
>>>>>>>>>> </Core::AlgorithmImplementation>
>>>>>>>>>></Core::Algorithm>
>>>>>>>>>>DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
>>>>>>>>>>("CORE"."ALGORITHM"."ROW_USER_ID") (DBD ERROR: OCIStmtExecute) at
>>>>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 137.
>>>>>>>>>>
>>>>>>>>>>SQL ERROR!! involving
>>>>>>>>>>
>>>>>>>>>> INSERT INTO Core.Algorithm (  description, other_read, user_write,
>>>>>>>>>>group_write, name, modification_date, user_read, algorithm_id,
>>>>>>>>>>row_alg_invocation_id, group_read, other_write )
>>>>>>>>>> VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>>>>>>>>>>Values: GUS application framework for plugins, 1, 1, 1, GA-Plugin, 1, 23,
>>>>>>>>>>1, 1, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 177.
>>>>>>>>>>[chetna@mango chetna]$
>>>>>>>>>>
>>>>>>>>>>Hope to hear from you
>>>>>>>>>>Chetna
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>               
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>>>
>>>>>>>>>             
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>-------------------------------------------------------
>>>>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
>>>>>>>>Get cracking and register here for some mind boggling fun and
>>>>>>>>the chance of winning an Apple iPod:
>>>>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
>>>>>>>>_______________________________________________
>>>>>>>>Gusdev-gusdev mailing list
>>>>>>>>Gus...@li...
>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>           
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>>-------------------------------------------------------
>>>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
>>>>>>>Get cracking and register here for some mind boggling fun and
>>>>>>>the chance of winning an Apple iPod:
>>>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
>>>>>>>_______________________________________________
>>>>>>>Gusdev-gusdev mailing list
>>>>>>>Gus...@li...
>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>         
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>-------------------------------------------------------
>>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
>>>>>>Get cracking and register here for some mind boggling fun and
>>>>>>the chance of winning an Apple iPod:
>>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
>>>>>>_______________________________________________
>>>>>>Gusdev-gusdev mailing list
>>>>>>Gus...@li...
>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>>-------------------------------------------------------
>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
>>>>>Get cracking and register here for some mind boggling fun and
>>>>>the chance of winning an Apple iPod:
>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>-------------------------------------------------------
>>>>This SF.net email is sponsored by:Crypto Challenge is now open! 
>>>>Get cracking and register here for some mind boggling fun and 
>>>>the chance of winning an Apple iPod:
>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>> 
>>>
>>>      
>>>
>>    
>>
>
>
>  
>

Re: [Gusdev-gusdev] Setting up your initial Users, etc

[Chetna W. <ch...@ar...>]

Hi Steve,

Thanks for the mail. As you said I changed userLogin == login of
core.userinfo so the error msg "ORA-01400: cannot insert NULL into
("CORE"."ALGORITHM"."ROW_USER_ID")" is gone. But now 

DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("CORE"."ALGORITHM"."ROW_GROUP_ID") (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 138.

is coming. I verified that core.groupinfo has "ctegd" as name and "2" as
its group_id but I am wondering  why's the ga getting null value

Hope to hear from you
chetna

> userName from gus.properties corresponds to the login attribute of 
> core.userinfo.
> 
> i know this is confusing (we have known about this but didn't get to 
> fixing it)
> 
> i think that we should consider renaming the property in .gus.property to:
>   userLogin=sfischer
> 
> the databaseLogin is something like this:
>   databaseLogin=GUSrw
> 
> meanwhile, i plan on improving the error message ga puts out in this 
> case so that it won't be hard to figure out what is going on.
> 
> steve
> 
> Chetna Warade wrote:
> 
> >Hi Dave,
> >
> >Yes I knew from gus 2.0 that the user in gus properties correspond to the
> >oracle user login. Is this true in gus 3.0 too - meaning databaseLogin in 
> >.gus.properties correspond to user_id in the core.userinfo. And is
> >userName any important (I did make the FIRST_NAME in Core.userinfo equal
> >to the $USER of .gus.properties).
> >
> >Thanks
> >Chetna
> >
> >  
> >
> >>Forgot to mention this the first time; is the user you added in
> >>Core.UserInfo the same as the one in your .gus.properties file?
> >>
> >>If it is, then sorry, that's probably the extent of my usefulness in
> >>solving this problem!
> >>
> >>dave
> >>
> >>On Fri, 14 Mar 2003, Chetna Warade wrote:
> >>
> >>    
> >>
> >>>Hi guys,
> >>>
> >>>Yes I added a user in Core.UserInfo and Sres.Contact, but I still getting
> >>>the same error for ga +meta --commit. Can anyone tell me what tables I
> >>>need for projects and groups, Are they Core.GroupInfo and
> >>>Core.ProjectInfo?. In the meantime I am adding rows in these two tables
> >>>but please let me know if there are other table dependencies.
> >>>
> >>>Thanks to all for the help
> >>>Chetna
> >>>
> >>>
> >>>      
> >>>
> >>>>yes, i agree.  chetna- you need to set up your Users and Projects, etc.
> >>>> Have you ever done this before?
> >>>>
> >>>>Jonathan Crabtree is away until Wed.  I don't know if he has set up
> >>>>scripts to assist in this process.  but, we should provide something to
> >>>>make this painless.
> >>>>
> >>>>I personally don't know the details of what is involved.
> >>>>
> >>>>Can anybody at PSU sketch what chetna should do?
> >>>>
> >>>>thanks
> >>>>steve
> >>>>
> >>>>Dave Barkan wrote:
> >>>>
> >>>>        
> >>>>
> >>>>>Hi Chetna and all,
> >>>>>
> >>>>>I had this problem too at one point.  Someone needs to insert Chetna into
> >>>>>our UserInfo table as a user and give her the appropriate permissions.
> >>>>>
> >>>>>Dave
> >>>>>
> >>>>>On Fri, 14 Mar 2003, Chetna Warade wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>          
> >>>>>
> >>>>>>Hi Steve,
> >>>>>>
> >>>>>>I got the latest tars today morning, but I am getting:
> >>>>>>
> >>>>>>[chetna@mango install]$ ga +meta --commit
> >>>>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> >>>>>>Reading properties from /home/chetna/.gus.properties
> >>>>>> <Core::Algorithm>
> >>>>>>   <name>GA-Plugin</name>
> >>>>>>   <description>GUS application framework for plugins</description>
> >>>>>>   <Core::AlgorithmImplementation>
> >>>>>>     <cvs_revision>1.36</cvs_revision>
> >>>>>>     <cvs_tag> </cvs_tag>
> >>>>>>     <executable>GUS::PluginMgr::GusApplication</executable>
> >>>>>>     <executable_md5>5947e17c4e9fea1d750cb5d9aaeee1db</executable_md5>
> >>>>>>     <description>update for GUS 3.0</description>
> >>>>>>     <Core::AlgorithmInvocation>
> >>>>>>       <start_time>sysdate</start_time>
> >>>>>>       <end_time>sysdate</end_time>
> >>>>>>       <machine_id>0</machine_id>
> >>>>>>       <cpus_used>1</cpus_used>
> >>>>>>       <result>meta</result>
> >>>>>>     </Core::AlgorithmInvocation>
> >>>>>>   </Core::AlgorithmImplementation>
> >>>>>> </Core::Algorithm>
> >>>>>>DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> >>>>>>("CORE"."ALGORITHM"."ROW_USER_ID") (DBD ERROR: OCIStmtExecute) at
> >>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 138.
> >>>>>>
> >>>>>>SQL ERROR!! involving
> >>>>>>
> >>>>>>   INSERT INTO Core.Algorithm (  description, other_read, user_write,
> >>>>>>group_write, name, modification_date, user_read, algorithm_id,
> >>>>>>row_alg_invocation_id, group_read, other_write )
> >>>>>>   VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >>>>>>Values: GUS application framework for plugins, 1, 1, 1, GA-Plugin, 1, 45,
> >>>>>>1, 1, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 178
> >>>>>>
> >>>>>>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x84ee5e8)',
> >>>>>>'^J SQL ERROR!! involving^J ^J    INSERT INTO Core.Algorithm (  desc...')
> >>>>>>called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 141
> >>>>>>
> >>>>>>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x84ee5e8)',
> >>>>>>'GUS::ObjRelP::DbiDbHandle::st=HASH(0x86b7f10)', 'ARRAY(0x86b7f64)', '^J
> >>>>>>INSERT INTO Core.Algorithm (  description, other_read, user...') called at
> >>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 694
> >>>>>>
> >>>>>>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::Algorithm=HASH(0x84ee42c)',
> >>>>>>'GUS::Model::Core::Algorithm', 'HASH(0x85f7aa0)') called at
> >>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 641
> >>>>>>
> >>>>>>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::Algorithm=HASH(0x84ee42c)')
> >>>>>>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >>>>>>
> >>>>>>GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x84ee42c)')
> >>>>>>called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 339
> >>>>>>
> >>>>>>GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>>>undef) called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>>>line 283
> >>>>>>
> >>>>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>>>undef) called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>>>line 192
> >>>>>>
> >>>>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>>>'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> >>>>>>[chetna@mango install]$
> >>>>>>
> >>>>>>Thanks,
> >>>>>>Chetna
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>            
> >>>>>>
> >>>>>>>can you get the install.tar and the gus.tar files again from cvsweb at
> >>>>>>>sanger.
> >>>>>>>
> >>>>>>>we have fixed an important problem that was introduced in the last few
> >>>>>>>days, and i think that will fix your problem.
> >>>>>>>
> >>>>>>>i just tested ga +meta --commit here and it seemed fine.
> >>>>>>>
> >>>>>>>steve
> >>>>>>>
> >>>>>>>Chetna Warade wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>              
> >>>>>>>
> >>>>>>>>Hi Steve,
> >>>>>>>>
> >>>>>>>>Thanks for the mail.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>
> >>>>>>>>>1) can you send me the lines that you commented, so i can fix the problem.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>                  
> >>>>>>>>>
> >>>>>>>>$GUS_HOME/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> >>>>>>>>line # 148
> >>>>>>>>line # 469
> >>>>>>>>line # 478
> >>>>>>>>Basically wherever string BIG (Actually BIGRBS1 in gus 3.0) appears.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>
> >>>>>>>>>2) the problem is that the tarball is excluding empty directories.  for
> >>>>>>>>>now, create the following directories:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>                  
> >>>>>>>>>
> >>>>>>>>Thanks build is working correct now. But here's what I get:
> >>>>>>>>
> >>>>>>>>[chetna@mango chetna]$ ga +meta --commit
> >>>>>>>>Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> >>>>>>>>Reading properties from /home/chetna/.gus.properties
> >>>>>>>><Core::Algorithm>
> >>>>>>>>  <name>GA-Plugin</name>
> >>>>>>>>  <description>GUS application framework for plugins</description>
> >>>>>>>>  <Core::AlgorithmImplementation>
> >>>>>>>>    <cvs_revision>1.33</cvs_revision>
> >>>>>>>>    <cvs_tag> </cvs_tag>
> >>>>>>>>    <executable>GUS::PluginMgr::GusApplication</executable>
> >>>>>>>>    <executable_md5>0f9925c1794c069d858378c052a9d747</executable_md5>
> >>>>>>>>    <description>update for GUS 3.0</description>
> >>>>>>>>    <Core::AlgorithmInvocation>
> >>>>>>>>      <start_time>sysdate</start_time>
> >>>>>>>>      <end_time>sysdate</end_time>
> >>>>>>>>      <machine_id>0</machine_id>
> >>>>>>>>      <cpus_used>1</cpus_used>
> >>>>>>>>      <result>meta</result>
> >>>>>>>>    </Core::AlgorithmInvocation>
> >>>>>>>>  </Core::AlgorithmImplementation>
> >>>>>>>></Core::Algorithm>
> >>>>>>>>DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> >>>>>>>>("CORE"."ALGORITHM"."ROW_USER_ID") (DBD ERROR: OCIStmtExecute) at
> >>>>>>>>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 137.
> >>>>>>>>
> >>>>>>>>SQL ERROR!! involving
> >>>>>>>>
> >>>>>>>>  INSERT INTO Core.Algorithm (  description, other_read, user_write,
> >>>>>>>>group_write, name, modification_date, user_read, algorithm_id,
> >>>>>>>>row_alg_invocation_id, group_read, other_write )
> >>>>>>>>  VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >>>>>>>>Values: GUS application framework for plugins, 1, 1, 1, GA-Plugin, 1, 23,
> >>>>>>>>1, 1, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 177.
> >>>>>>>>[chetna@mango chetna]$
> >>>>>>>>
> >>>>>>>>Hope to hear from you
> >>>>>>>>Chetna
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>
> >>>>>>>              
> >>>>>>>
> >>>>>>-------------------------------------------------------
> >>>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>>>>Get cracking and register here for some mind boggling fun and
> >>>>>>the chance of winning an Apple iPod:
> >>>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>>>_______________________________________________
> >>>>>>Gusdev-gusdev mailing list
> >>>>>>Gus...@li...
> >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>            
> >>>>>>
> >>>>>
> >>>>>-------------------------------------------------------
> >>>>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>>>Get cracking and register here for some mind boggling fun and
> >>>>>the chance of winning an Apple iPod:
> >>>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>>_______________________________________________
> >>>>>Gusdev-gusdev mailing list
> >>>>>Gus...@li...
> >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>          
> >>>>>
> >>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>>Get cracking and register here for some mind boggling fun and
> >>>>the chance of winning an Apple iPod:
> >>>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>>        
> >>>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.net email is sponsored by:Crypto Challenge is now open!
> >>>Get cracking and register here for some mind boggling fun and
> >>>the chance of winning an Apple iPod:
> >>>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>>_______________________________________________
> >>>Gusdev-gusdev mailing list
> >>>Gus...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>
> >>>      
> >>>
> >>
> >>-------------------------------------------------------
> >>This SF.net email is sponsored by:Crypto Challenge is now open! 
> >>Get cracking and register here for some mind boggling fun and 
> >>the chance of winning an Apple iPod:
> >>http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>    
> >>
> >
> >
> >  
> >
> 
> 

Re: [Gusdev-gusdev] plugin inventory

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

keith-

i have attached below the set of plugins that exist in our old cvs. 
these, in addition to the ones in the current cvs under */*/plugin are 
the totality.   besides fasta and blat, i am not sure they cover any on 
your list.  plugins that haven't been moved to the new cvs are 
definitely not gus 3.0 compliant.

if you guys are going to gear up to write this number of plugins, i 
think it might make sense to ask how much do they have in common, and 
consider developing a small api to help out (or extend the plugin api). 
 i would be willing to assist in this.

steve

ps, sorry for the delay in answering.

AddPredictedSequences.pm                    LoadBlastSim4.pm
AnnotatorsInterfaceSubmitter.pm*            LoadBlastSimilaritiesPK.pm
AssemblyProteinInstance.pm                  LoadBLATAlignments.pm
AssignAASequenceCellRoles.pm                LoadCenTelo.pm
AssignEGADCellRoles.pm                      LoadCorePromoter.pm
AssignLibraryDistributionToAssemblies.pm    LoadEndSequencePairs.pm
AssignRNANameAndDescription.pm              LoadEPCR.pm*
AssignSequenceDescription.pm                LoadEpitopeFeatures.pm
BaseComposition.pm                          LoadFromTigrXml.pm
CalculateAASeqVariations.pm                 LoadGadflyRelease.pm
CalculateGeneFeatureESTOverlaps.pm          LoadGeneFeaturesFromEMBL.pm
CalculateGeneFeatureSAGETagLinks.pm         LoadGeneFeaturesFromGenBank.pm
CalculateGeneFeatureSeqOverlaps.pm          LoadGeneFeaturesFromXML.pm
CalculateGeneTrapLinks.pm                   LoadGoldenPathVirSeq.pm
ChangeGenBankGeneFeatures.pm                LoadGoOntology.pm
CheckAndFixCodingStart.pm                   LoadLowComplexityAAFeatures.pm
ConvertSequenceGapsToGappedSequence.pm      LoadLowComplexityNAFeatures.pm
CopyAASeqGoFuncToProtGoFunc.pm              LoadMGIInfo.pm
CopyCRAndGOFToAASequence.pm                 LoadNRDB.pm
CorrPositions.pm                            LoadORNLDraftGenePredictions.pm
CreateAllGenesStatistics.pm                 LoadOrnlPredictions.pm
CreateCloneSet.pm                           LoadPromRec.pm
CreateUCSCVirtualChromosomes.pm             LoadrRNAs.pm
CreateVirtualSequence.pm                    LoadTaxon.pm
CrossMatch.pm                               LoadTrnas.pm
CVS/                                        LoadWms.pm
DeleteAssembliesWithNoAssemblySequences.pm  LoadWorkflowFromXML.pm
DeleteBadAssemblies.pm                      MakeAAFeaturesForAssemblies.pm
DeleteDuplicatedAssemblySequences.pm        MakeAssemblySequences.pm
DeleteGenePredictions.pm                    MakeGoPredictionRules.pm
DeleteGoPredictions.pm                      MakeGoPredictions.pm
DeleteSimilarities.pm                       MakeIndexWordLink.pm
DisplayTable.pm                             MakeIndexWordSimLink.pm
DocumentTables.pm                           MakeProjectLink.pm
ExtractAndBlockAssemblySequences.pm         MakeRNAAnddProtein.pm
ExtractEsts.pm                              MakeRNAAndProtein.pm
ExtractPromoters.pm                         MakeRNAClustersForAssemblies.pm
FixCodingStart.pm                           ManageGoRules.pm
FixLibdbEST.pm                              MarkAssemblySequencesBad.pm
FixMissingNASequenceIds.pm                  MergeGenes.pm
FixSequenceLength.pm                        MouseGeneMap.pm*
FixStemCellIds.pm                           MoveSimilaritiesToAssembly.pm
FixStroCDBExtDbId.pm                        OpticalMapMatch.pm
FrameFinder.pm                              PointSimilaritiesToNewTable.pm
GBParser.pm                                 ReassembleDOTSRNA.pm
GenePlotReport.pm                           RemoveDeletedAssemblies.pm
GenerateSageTags.pm                         RepeatMaskSequence.pm
GoComparison.pm                             ReplaceChars.pm
IdentifyAndLoadSnpsFromAssemblies.pm        RestrictionDigest.pm
ImportCloneSeqDbest.pm                      RestrictionDigestSeqs.pm
ImportFpcFlatfile.pm                        RNAProteinIntegration.pm
ImportLibDbest.pm                           SetAssSeqQualStartStop.pm
ImportNASequences.pm                        Sim4.pm
ImportPfam.pm                               StartWorkflow.pm*
ImportPlasmoDBPrediction.pm                 Template.pm
ImportSangerPredictionsFromGFF.pm           TessLoadGoldenPathRepeats.pm
InsertDbRefAndDbRefNASequence.pm            TestUpdateEfficiency.pm
InsertNewExternalNASequences.pm             triv_trans.pm
InsertNewExternalNRDBSequences.pm           UpdateDotsAssembliesWithCap4.pm
InsertNewExternalSequences.pm               UpdateGeneAndRNAConf.pm
InsertSubSeq.pm                             UpdateGusFromXML.pm*
InsertWorkflowInit.pm                       VersionAndDeleteSimilarities.pm
LinkGenesToRNAs.pm                          WipeGeneFeaturePredictions.pm
LoadArachneAssembly.pm                      WipeORNLPredictions.pm
LoadBdgpRelease.pm



Keith James wrote:

>Hi,
>
>I'm looking into the inventory of Perl module plugins which we could
>possibly need to perform our standard analyses on data housed in
>GUS. I've jotted down a list below. For the purposes of planning at
>our end, I'd be interested in knowing if any of these either exist or
>are planned.
>
>blast (I know this exists)
>blat
>fasta
>repeatmasker
>seg
>reputer
>glimmer(m)
>phat
>geneid
>hmmgene
>genewise/estwise etc.
>tRNAscan-SE
>infernal
>emboss programs (any)
>hmmer/hmmpfam
>FingerPRINTScan
>pfscan
>tmhmm
>signalp
>clustal
>DNA block aligner
>TCoffee
>
>thanks,
>
>Keith
>
>  
>

Re: [Gusdev-gusdev] JSP / Object mechanism

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

my initial response:  now that you mention Struts, i recall that 
DoubleTwist used it for their web arch.  They were enthusiatic about it, 
but the project fell with the company.  anyway, absent any knowledge of 
its details, it seems definitely worth looking seriously at.

steve

pjm wrote:

>All,
>
>We have been thinking about the jsp-object part of the web interface. The
>fact the jsp pages will require data from several sources including the
>GUS DB, Perl programs, flat files (config files, XML), other internet
>resources, etc, etc means that the mechanism for controlling this
>communication needs to be structured.
>
>We have been looking at Jakarta Struts (http://jakarta.apache.org/struts/)
>because we think this could help us structure, manage and simplify the way
>the jsp talks to the various objects. Several groups here at Hinxton use it
>in anger and say good things about it.
>
>It provides a prewritten and tested framework which broadly fits the model
>Steve sent us. In particular the tiles code, for separating content and
>presentation with easy centralised configuration of the later would seem
>to be an ideal fit with our joint requirements.
>
>To learn more about Struts I suggest you start at;
>http://www.onjava.com/pub/a/onjava/excerpt/progjakstruts_14/index1.html
>and work your way through the 4 articles in the series.
>
>There are several books available on Struts, we've been reading the
>O'Reilly version. So far myself and Adrian like what we see. If you do too
>we would like to code, or at least outline in reasonable depth, an example
>for the Query Results page since it will be similar for both groups.
>
>What do you think?
>
>
>Paul.
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: Tablet PC.  
>Does your code think in ink? You could win a Tablet PC. 
>Get a free Tablet PC hat just for playing. What are you waiting for? 
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>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>  
>

[Gusdev-gusdev] JSP / Object mechanism

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

All,

We have been thinking about the jsp-object part of the web interface. The
fact the jsp pages will require data from several sources including the
GUS DB, Perl programs, flat files (config files, XML), other internet
resources, etc, etc means that the mechanism for controlling this
communication needs to be structured.

We have been looking at Jakarta Struts (http://jakarta.apache.org/struts/)
because we think this could help us structure, manage and simplify the way
the jsp talks to the various objects. Several groups here at Hinxton use it
in anger and say good things about it.

It provides a prewritten and tested framework which broadly fits the model
Steve sent us. In particular the tiles code, for separating content and
presentation with easy centralised configuration of the later would seem
to be an ideal fit with our joint requirements.

To learn more about Struts I suggest you start at;
http://www.onjava.com/pub/a/onjava/excerpt/progjakstruts_14/index1.html
and work your way through the 4 articles in the series.

There are several books available on Struts, we've been reading the
O'Reilly version. So far myself and Adrian like what we see. If you do too
we would like to code, or at least outline in reasonable depth, an example
for the Query Results page since it will be similar for both groups.

What do you think?


Paul.