gusdev-gusdev — Topics concerning GUS development

[Gusdev-gusdev] updated UpdateGusFromXML

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

Hi all,
this is to let you know that I've applied the changes proposed below and
also that I've added a couple more lines which this plugin will print to
STDOUT (when the plugin does not exit on error). These lines start
respectively with "INSERTED (non-overhead)" and "UPDATED (non-overhead)"
and denote the number of inserted (resp. updated) objects, without
counting the overhead ones (e.g. AlgorithmInvocation etc.).
I've cvs committed the plugin.
Elisabetta

On Tue, 18 Mar 2003, steve fischer wrote:

> folks-
>
> elisabetta and i have discovered a suspicious line of code in
> UpdateGusFromXML:
>
>     ##testing exitOnFailure...
>     $self->getDb()->setExitOnSQLFailure(0);
>
> this will cause the plugin to continue processing the xml file even
> after one of the included transactions fails and rollsback.
>
> if somebody wants this behavior then this should be made into a command
> line option.
>
> otherwise, unless somebody can provide reaons otherwise, we are going to
> remove that line of code, forcing the parse of XML to die if there is a
> problem so that the user of the plugin will be aware of and correct the
> problem.
>
> steve
>

-- 
Elisabetta Manduchi

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

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

---

[Gusdev-gusdev] NEW FUNCTIONALITY for Perl Object Layer

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

folks-

With some suggestions from Brian, Dave and I have embarked on coding a 
new feature in the Perl Object Layer (which Dave will presumably include 
in the Java layer).  We will be able to add children or parents based on 
the name of the attribute in the child which holds the foreign key.  In 
other words, the object layer will fully support parents (children) 
having more than one kind of relationship to a particular child (parent) 
table.  

An existing example of this is:  
   BLATAlignment is the child of NASequenceImp with the two attributes: 
target_na_sequence_id and its query_na_sequence_id.

We will maintain backward compatibility (but will be doing away with the 
modelSpecialCases file).

An example of the functionality is:
$obj->setChild($child);           # old style, still supported
$obj->setChild($child, "AttributeName")    # the child is set using 
AttributeName.  only nec. if more than one relationship with the child 
table exists.

In the example of BLATAlignment:
   $BLATalign->setParent($naseq)      # will cause an error because this 
relationship needs the attribute name to disambiguate.
   $BLATalign->setParent($naseq, "QueryNaSequence");



The stategic question we NEED YOUR FEEDBACK ON is when should we merge 
this change into the main codebase?

We would like to do it as soon as we can (the longer we wait, the harder 
will be our code merge), but without putting at risk projects that have 
critical deadlines.

We know that the RAD folks may need this, and LoadGOOntology.

steve

Re: [Gusdev-gusdev] LoadGoOntology Plugin

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

Hey Arnaud,

I think you are correct about the incorrect type of the GO Id.  I'll have
a look and see if I can apply a fix.

Dave

On Tue, 18 Mar 2003, Arnaud Kerhornou wrote:

> Hi
>
> I'm testing the LoadGoOntology plugin to load the GO component ontology.
>
> The CBIL archive, CBIL_v1-2-0.tar.gz, has the following path,
> CBIL/Bio/lib/perl/GeneOntolgyParser where GeneOntologyParser is misspelled.
>
> I renamed the directory to be able to test the plugin but the run stops
> at some point :
>
> -------------------------->
>
> >ga GUS::GOPredict::Plugin::LoadGoOntology --verbose --flat_file=component.ontology --file_path=/nfs/pathsoft/databases/go_cvs/ontology --id_file=2.318
>
> sqlExec:
>     INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, group_write, ancestor_go_term_id, row_project_id, name, external_database_release_id, is_obsolete, group_read, minimum_level, row_group_id, go_term_id, other_read, source_id, modification_date, user_read, row_alg_invocation_id, number_of_levels, maximum_level, definition, other_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? )
>   bindValues (1, GO:0000325, 1, 1, GO:0005575, 1, vacuole (sensu Magnoliophyta), 228, 0, 1, 6, 1, 1, 1, GO:0000325, 1, 4, 1, 6, vacuole (sensu Magnoliophyta), 0)
> DBD::Oracle::st execute failed: ORA-01722: invalid number (DBD ERROR: OCIStmtExecute) at /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 139.
>
> <--------------------------
>
> I think it's because of "ancestor_go_term_id" which expects a number and gets "GO:0005575" a GO term instead of the Primary Key for this GO ancestor term.
>
> Can someone have a look at it ?
>
> cheers
> Arnaud
>
>
>
>
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[Gusdev-gusdev] LoadGoOntology Plugin

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

Hi

I'm testing the LoadGoOntology plugin to load the GO component ontology.

The CBIL archive, CBIL_v1-2-0.tar.gz, has the following path, 
CBIL/Bio/lib/perl/GeneOntolgyParser where GeneOntologyParser is misspelled.

I renamed the directory to be able to test the plugin but the run stops 
at some point :

-------------------------->

>ga GUS::GOPredict::Plugin::LoadGoOntology --verbose --flat_file=component.ontology --file_path=/nfs/pathsoft/databases/go_cvs/ontology --id_file=2.318

sqlExec: 
    INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, group_write, ancestor_go_term_id, row_project_id, name, external_database_release_id, is_obsolete, group_read, minimum_level, row_group_id, go_term_id, other_read, source_id, modification_date, user_read, row_alg_invocation_id, number_of_levels, maximum_level, definition, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
  bindValues (1, GO:0000325, 1, 1, GO:0005575, 1, vacuole (sensu Magnoliophyta), 228, 0, 1, 6, 1, 1, 1, GO:0000325, 1, 4, 1, 6, vacuole (sensu Magnoliophyta), 0)
DBD::Oracle::st execute failed: ORA-01722: invalid number (DBD ERROR: OCIStmtExecute) at /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 139.

<--------------------------

I think it's because of "ancestor_go_term_id" which expects a number and gets "GO:0005575" a GO term instead of the Primary Key for this GO ancestor term.

Can someone have a look at it ?

cheers
Arnaud

[Gusdev-gusdev] UpdateGusFromXML: proposed CHANGE

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

folks-

elisabetta and i have discovered a suspicious line of code in 
UpdateGusFromXML:

    ##testing exitOnFailure...
    $self->getDb()->setExitOnSQLFailure(0);

this will cause the plugin to continue processing the xml file even 
after one of the included transactions fails and rollsback.

if somebody wants this behavior then this should be made into a command 
line option.

otherwise, unless somebody can provide reaons otherwise, we are going to 
remove that line of code, forcing the parse of XML to die if there is a 
problem so that the user of the plugin will be aware of and correct the 
problem.

steve

Re: [Gusdev-gusdev] mail problems?

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

No problems with the gusdev list mail.



On Sat, 15 Mar 2003, Steve Fischer wrote:

> is anybody besides Chetna having problems sending or receiving mail to
> the gusdev list?
>
> steve
>
>
>
> -------------------------------------------------------
> 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:
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> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] test mail

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

test

[Gusdev-gusdev] mail problems?

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

is anybody besides Chetna having problems sending or receiving mail to 
the gusdev list?

steve

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

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

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
>>>_______________________________________________
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>>>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:
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>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>  
>

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

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

Hi 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
>

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

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

Please disregard my previous message on the RADform submission. That has
only to do with our copy of GUS. Sorry.
In any case, the tables for project and group should be Core.ProjectInfo
and Core.GroupInfo.
Elisabetta

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
>

-- 
Elisabetta Manduchi

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

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

---

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

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

steve fischer wrote:
> 
> 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?

Arnaud setup the DB but I don't *think* he did anything specail.

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

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

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
> 

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

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

In the RADwebform we have a user registration submission:

https://www.cbil.upenn.edu/RAD/forms/php/misc/user_registration.php

This will send email to Trish Whetzel with all the the necessary
information and she can start the process of creating  a user account.
Elisabetta

On Fri, 14 Mar 2003, steve fischer wrote:

> 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
>

-- 
Elisabetta Manduchi

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

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

---

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

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

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:
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>
>
>  
>

Re: [Gusdev-gusdev] Re: Hi

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

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
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] Re: Hi

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

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
> >
> >
> >
> >  
> >
> 
> 

Re: [Gusdev-gusdev] The Way to test a plugin

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

Steve,

I've done a 'cvs update' and "build GUS install -append' so everything is
up-to-date and in sync.

I get a circular thing happening when told to
	'ga +update GUS::PluginMgr::GusApplication --commit'
It keeps telling me to do it when it doesn't work! What should I do?

See;

pcs2b[pjm]136: ga +update GUS::Common::Plugin::LoadPfam --commit
Reading properties from /nfs/team81/pjm/GUS/config/GUS-PluginMgr.prop
Reading properties from /nfs/team81/pjm/.gus.properties
DBD::Oracle::db do failed: ORA-01534: rollback segment 'BIGRBS1' doesn't exist
(DBD ERROR: OCIStmtExecute) at
/nfs/team81/pjm/GUS/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 148.

USER ERROR: No Core.AlgorithmImplementation found for
GUS::PluginMgr::GusApplication cvs revision 1.35. 
Please use 'ga +update GUS::PluginMgr::GusApplication --commit'
pcs2b[pjm]137: 
pcs2b[pjm]137: ga +update GUS::PluginMgr::GusApplication --commit
Reading properties from /nfs/team81/pjm/GUS/config/GUS-PluginMgr.prop
Reading properties from /nfs/team81/pjm/.gus.properties
DBD::Oracle::db do failed: ORA-01534: rollback segment 'BIGRBS1' doesn't exist
(DBD ERROR: OCIStmtExecute) at
/nfs/team81/pjm/GUS/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 148.

USER ERROR: No Core.AlgorithmImplementation found for
GUS::PluginMgr::GusApplication cvs revision 1.35. 
Please use 'ga +update GUS::PluginMgr::GusApplication --commit'



steve fischer wrote:
> 
> sorry paul that we just haven't gotten to documenting this.
> 
> here is the sequence:
> 
> 1. write the plugin initially
> 2. check it in to cvs first time
> 3. build
> 4. ga +create PLUGIN --commit
> 5. now you can debug and tweek your plugin by running ga PLUGIN (without
> --commit)
> 6. when it is working enough to test with --commit:
>         - check it in to cvs
>         - build
>         - ga +update PLUGIN --commit
> 7. iterarate on steps 5 and 6
> 
> steve
> 
> pjm wrote:
> 
> >Steve,
> >
> >Ok, I dug out your old email on --commit registering plugins to find The Way of
> >testing my LoadPfam plugin with a tiny subsection of the latest PFma release. It
> >only creates records a few tables and they are all currently empty in my DB.
> >Anything it creates I will quite happily (and easily) destroy (drop 3 tables).
> >
> >Thus, before I cvs commit I wanted to try out --commit. But I can't run it with
> >out cvs commiting...
> >
> >I take it I can cvs commit, then `ga +update GUS::Common::Plugin::LoadPfam` as
> >needed, right?
> >
> >UPDATE
> >
> >I cvs commited the code so far (it needs a tidy, some print statements removing)
> >but its more or less there. Thinking it would get around the --commit problems I
> >did a
> >
> >       `ga +update GUS::Common::Plugin::LoadPfam`
> >
> >but because its already registered it won't update it. Doh! How do I get around
> >this? What is The Way?
> >
> >Paul.
> >
> >steve fischer wrote:
> >
> >
> >>just want to clarify why debbie "committed when i should not have".
> >>
> >>the deal is that we are extremely rigorous about our tracking of bulk
> >>changes to the db.
> >>
> >>in particular, you cannot run a plugin with --commit unless that exact
> >>revision of the plugin has been registered in the db.  and, you cannot
> >>do that registering unless you have checked in that version of the
> >>plugin to cvs.
> >>
> >>instead of checking in a crippled version of a plugin, hacks like this
> >>can be accomplished by other ways, such as:
> >>  - introducing a temporary command line arg which the plugin tests for
> >>to run its hacky code.
> >>  - copying the plugin to a new file, such as LoadTaxonDebbiesHack.pm,
> >>and registering it as a new plugin
> >>
> >>steve
> >>
> >>Deborah F. Pinney wrote:
> >>
> >>
> >>
> >>>This is my fault. I commited to cvs when I should not have. I have
> >>>uncommented those lines and recomitted to cvs.
> >>>
> >>>
> >>>                                               Deboeah Pinney
> >>>
> >>>
> >>>On Wed, 5 Mar 2003, Arnaud
> >>>Kerhornou wrote:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>Hi
> >>>>
> >>>>I'm trying to run LoadTaxon plugin. Why some lines are commented out ?
> >>>>
> >>>>   #my $genCodes = $self->makeGeneticCode();
> >>>>
> >>>>   my $namesDmp = $self->getNames();
> >>>>
> >>>>   #my $nodesHash = $self->makeNodesHash($genCodes);
> >>>>
> >>>>   #my $rootAttArray = $self->getRootAttArray($genCodes);
> >>>>
> >>>>   #$self->makeTaxonEntry($rootAttArray, \$count);
> >>>>
> >>>>   #if ($self->getCla->{'restart'} && $self->getCla->{'restart'} > 1) {
> >>>>     #$self->getTaxonAtt($self->getCla->{'restart'},$nodesHash,\$count);
> >>>>   #}
> >>>>   #else {
> >>>>     #$self->getTaxonAtt($rootAttArray->[0],$nodesHash,\$count);
> >>>>   #}
> >>>>
> >>>>Arnaud
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> >>>>for complex code. Debugging C/C++ programs can leave you feeling lost and
> >>>>disoriented. TotalView can help you find your way. Available on major UNIX
> >>>>and Linux platforms. Try it free. www.etnus.com
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> >>>for complex code. Debugging C/C++ programs can leave you feeling lost and
> >>>disoriented. TotalView can help you find your way. Available on major UNIX
> >>>and Linux platforms. Try it free. www.etnus.com
> >>>_______________________________________________
> >>>Gusdev-gusdev mailing list
> >>>Gus...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>-------------------------------------------------------
> >>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> >>for complex code. Debugging C/C++ programs can leave you feeling lost and
> >>disoriented. TotalView can help you find your way. Available on major UNIX
> >>and Linux platforms. Try it free. www.etnus.com
> >>_______________________________________________
> >>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:
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] The Way to test a plugin

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

sorry paul that we just haven't gotten to documenting this.

here is the sequence:

1. write the plugin initially
2. check it in to cvs first time
3. build
4. ga +create PLUGIN --commit
5. now you can debug and tweek your plugin by running ga PLUGIN (without 
--commit)
6. when it is working enough to test with --commit:  
        - check it in to cvs
        - build
        - ga +update PLUGIN --commit
7. iterarate on steps 5 and 6

steve


pjm wrote:

>Steve,
>
>Ok, I dug out your old email on --commit registering plugins to find The Way of
>testing my LoadPfam plugin with a tiny subsection of the latest PFma release. It
>only creates records a few tables and they are all currently empty in my DB.
>Anything it creates I will quite happily (and easily) destroy (drop 3 tables).
>
>Thus, before I cvs commit I wanted to try out --commit. But I can't run it with
>out cvs commiting...
>
>I take it I can cvs commit, then `ga +update GUS::Common::Plugin::LoadPfam` as
>needed, right? 
>
>UPDATE
>
>I cvs commited the code so far (it needs a tidy, some print statements removing)
>but its more or less there. Thinking it would get around the --commit problems I
>did a
>
>	`ga +update GUS::Common::Plugin::LoadPfam`
>
>but because its already registered it won't update it. Doh! How do I get around
>this? What is The Way?
>
>Paul.
>
>steve fischer wrote:
>  
>
>>just want to clarify why debbie "committed when i should not have".
>>
>>the deal is that we are extremely rigorous about our tracking of bulk
>>changes to the db.
>>
>>in particular, you cannot run a plugin with --commit unless that exact
>>revision of the plugin has been registered in the db.  and, you cannot
>>do that registering unless you have checked in that version of the
>>plugin to cvs.
>>
>>instead of checking in a crippled version of a plugin, hacks like this
>>can be accomplished by other ways, such as:
>>  - introducing a temporary command line arg which the plugin tests for
>>to run its hacky code.
>>  - copying the plugin to a new file, such as LoadTaxonDebbiesHack.pm,
>>and registering it as a new plugin
>>
>>steve
>>
>>Deborah F. Pinney wrote:
>>
>>    
>>
>>>This is my fault. I commited to cvs when I should not have. I have
>>>uncommented those lines and recomitted to cvs.
>>>
>>>
>>>                                               Deboeah Pinney
>>>
>>>
>>>On Wed, 5 Mar 2003, Arnaud
>>>Kerhornou wrote:
>>>
>>>
>>>
>>>      
>>>
>>>>Hi
>>>>
>>>>I'm trying to run LoadTaxon plugin. Why some lines are commented out ?
>>>>
>>>>   #my $genCodes = $self->makeGeneticCode();
>>>>
>>>>   my $namesDmp = $self->getNames();
>>>>
>>>>   #my $nodesHash = $self->makeNodesHash($genCodes);
>>>>
>>>>   #my $rootAttArray = $self->getRootAttArray($genCodes);
>>>>
>>>>   #$self->makeTaxonEntry($rootAttArray, \$count);
>>>>
>>>>   #if ($self->getCla->{'restart'} && $self->getCla->{'restart'} > 1) {
>>>>     #$self->getTaxonAtt($self->getCla->{'restart'},$nodesHash,\$count);
>>>>   #}
>>>>   #else {
>>>>     #$self->getTaxonAtt($rootAttArray->[0],$nodesHash,\$count);
>>>>   #}
>>>>
>>>>Arnaud
>>>>
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>>>>for complex code. Debugging C/C++ programs can leave you feeling lost and
>>>>disoriented. TotalView can help you find your way. Available on major UNIX
>>>>and Linux platforms. Try it free. www.etnus.com
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>>>for complex code. Debugging C/C++ programs can leave you feeling lost and
>>>disoriented. TotalView can help you find your way. Available on major UNIX
>>>and Linux platforms. Try it free. www.etnus.com
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>>
>>>      
>>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>>for complex code. Debugging C/C++ programs can leave you feeling lost and
>>disoriented. TotalView can help you find your way. Available on major UNIX
>>and Linux platforms. Try it free. www.etnus.com
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>    
>>
>
>
>  
>

Re: [Gusdev-gusdev] Re: gusdev mailing list subscription

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

I've have been having a similar problem.

On Fri, 14 Mar 2003, pjm wrote:

>
> I think I did `cvs update -d`, where -d creates any new directories. CVS won't
> create them by default, assuming you may only have checked out a subset of the
> code;
>
>        Use the -d option to create any directories that exist in the reposi-
>        tory if they're missing from the working directory.  (Normally, update
>        acts only on directories and files that were already enrolled in your
>        working directory.)  This is useful for updating directories that were
>        created in the repository since the initial checkout; but it has an
>        unfortunate side effect.  If you deliberately avoided certain direc-
>        tories in the repository when you created your working directory
>        (either through use of a module name or by listing explicitly the
>        files and directories you wanted on the command line), then updating
>        with -d will create those directories, which may not be what you want.
>
>
>
> steve fischer wrote:
> >
> > chetna-
> >
> > 1) can you send me the lines that you commented, so i can fix the problem.
> >
> > 2) the problem is that the tarball is excluding empty directories.  for
> > now, create the following directories:
> >
> > /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/SRes
> > /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/Core
> > /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/RAD3
> > /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/TESS
> >
> > steve
> >
> > Chetna Warade wrote:
> >
> > >Hi Steve,
> > >
> > >1) I downloaded latest tars from cvsweb sanger and tried to "build GUS
> > >install -append". I remember reading about the rollback segments some
> > >weeks back but in my case I need to comment 3 lines from
> > >$GUS_HOME/lib/perl/GUS/ObjRelP/ DbiDatabase.pm file.
> > >
> > >2)  But while building:
> > >.....
> > >     [copy] Copying 2 files to
> > >/home/projects/GUS/Model/src/java/org/gusdb/model/DoTS
> > >
> > >BUILD FAILED
> > >file:/home/projects/GUS/build.xml:123:
> > >/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/SRes not
> > >found.
> > >
> > >Because SRes is not there? Any idea I downloaded from cvsweb sanger today
> > >morning.
> > >
> > >Thanks for the help
> > >Chetna
> > >
> > >
> > >
> > >>ok, i see how i confused you.  what i described works for folks that are
> > >>using the cvs repository directly.
> > >>
> > >>in your case, instead, you should just get the new .tar files for GUS
> > >>and install from
> > >>
> > >> http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/GUS.tar.gz?cvsroot=GUS&f=h&tarball=1
> > >>and from
> > >>
> > >> http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/install/install.tar.gz?cvsroot=GUS&f=h&tarball=1
> > >>
> > >>hopefully, that will fix your problem.  otherwise, let me know.
> > >>
> > >>steve
> > >>
> > >>Chetna Warade wrote:
> > >>
> > >>
> > >>
> > >>>Hi,
> > >>>
> > >>>Thanks for the mail,
> > >>>
> > >>>1) I am little confused here about the rehash and updateAllProjects
> > >>>command.
> > >>>Where does these two commands/plugins/scripts live. I mean are they
> > >>>located in $GUS_HOME/bin directory..
> > >>>
> > >>>Also currently I haven't added the cvs on the $PROJECT/install and
> > >>>$PROJECT/GUS directories but in other repository to keep track of
> > >>>downloads at my side. So do you recommend putting it in $PROJECT install
> > >>>and GUS directories.
> > >>>
> > >>>2) I am still getting this:
> > >>>
> > >>>[chetna@mango chetna]$ ga +meta --commit
> > >>>Can't locate object method "userError" via package "GUS::Plugin
> > >>>on" (perhaps you forgot to load "GUS::PluginMgr::GusApplication
> > >>>home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> > >>>[chetna@mango chetna]$
> > >>>
> > >>>Hope to hear from you
> > >>>Chetna
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>>$PROJECT_HOME contains the projects:  GUS, install, CBIL, etc.  GUS and
> > >>>>install have CVS/ dirs, but CBIL doesn't because it is from the download
> > >>>>site.
> > >>>>
> > >>>>steve
> > >>>>
> > >>>>Chetna Warade wrote:
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>>Hi,
> > >>>>>
> > >>>>>I tried:
> > >>>>>[chetna@mango chetna]$ ga +meta --commit
> > >>>>>Can't locate object method "userError" via package
> > >>>>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
> > >>>>>"GUS::PluginMgr::GusApplication"?) at
> > >>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> > >>>>>[chetna@mango chetna]$
> > >>>>>
> > >>>>>Also to run cvs update do you expect a cvs system on the $PROJECT_HOME and
> > >>>>>$GUS_HOME directories.
> > >>>>>
> > >>>>>I will send a test mail on the gusdev-gusdev-list,
> > >>>>>
> > >>>>>Thanks,
> > >>>>>Chetna
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>>i don't think there are any resitrictions on who can write to the
> > >>>>>>mailing list.  what address are you trying, and what happens?
> > >>>>>>
> > >>>>>>as far as ga is concerned, first, the command is ga +meta --commit (not
> > >>>>>>--create).
> > >>>>>>
> > >>>>>>also, i think you should just make sure you have the latest.
> > >>>>>>
> > >>>>>>do this:
> > >>>>>>1. get the latest CBIL download from:
> > >>>>>>http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz
> > >>>>>>2. cd $PROJECT_HOME/install
> > >>>>>>     cvs update
> > >>>>>>     rehash
> > >>>>>>     updateAllProjects
> > >>>>>>
> > >>>>>>steve
> > >>>>>>
> > >>>>>>Chetna Warade wrote:
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>>Hi,
> > >>>>>>>
> > >>>>>>>I am trying to mail to the mailing list and I am unable to do so. I am
> > >>>>>>>wondering if I have enough permissions on the mail list.
> > >>>>>>>
> > >>>>>>>I am tyring to run:
> > >>>>>>>
> > >>>>>>>[chetna@mango chetna]$ ga +meta --create
> > >>>>>>>Can't locate object method "userError" via package
> > >>>>>>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
> > >>>>>>>"GUS::PluginMgr::GusApplication"?) at
> > >>>>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> > >>>>>>>[chetna@mango chetna]$
> > >>>>>>>
> > >>>>>>>It would be great if you could help me debug this.
> > >>>>>>>Thanks
> > >>>>>>>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
>

-- 
Elisabetta Manduchi

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

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

---

Re: [Gusdev-gusdev] Re: gusdev mailing list subscription

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

I think I did `cvs update -d`, where -d creates any new directories. CVS won't
create them by default, assuming you may only have checked out a subset of the
code;

       Use the -d option to create any directories that exist in the reposi-
       tory if they're missing from the working directory.  (Normally, update
       acts only on directories and files that were already enrolled in your
       working directory.)  This is useful for updating directories that were
       created in the repository since the initial checkout; but it has an
       unfortunate side effect.  If you deliberately avoided certain direc-
       tories in the repository when you created your working directory
       (either through use of a module name or by listing explicitly the
       files and directories you wanted on the command line), then updating
       with -d will create those directories, which may not be what you want.



steve fischer wrote:
> 
> chetna-
> 
> 1) can you send me the lines that you commented, so i can fix the problem.
> 
> 2) the problem is that the tarball is excluding empty directories.  for
> now, create the following directories:
> 
> /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/SRes
> /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/Core
> /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/RAD3
> /home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/TESS
> 
> steve
> 
> Chetna Warade wrote:
> 
> >Hi Steve,
> >
> >1) I downloaded latest tars from cvsweb sanger and tried to "build GUS
> >install -append". I remember reading about the rollback segments some
> >weeks back but in my case I need to comment 3 lines from
> >$GUS_HOME/lib/perl/GUS/ObjRelP/ DbiDatabase.pm file.
> >
> >2)  But while building:
> >.....
> >     [copy] Copying 2 files to
> >/home/projects/GUS/Model/src/java/org/gusdb/model/DoTS
> >
> >BUILD FAILED
> >file:/home/projects/GUS/build.xml:123:
> >/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/SRes not
> >found.
> >
> >Because SRes is not there? Any idea I downloaded from cvsweb sanger today
> >morning.
> >
> >Thanks for the help
> >Chetna
> >
> >
> >
> >>ok, i see how i confused you.  what i described works for folks that are
> >>using the cvs repository directly.
> >>
> >>in your case, instead, you should just get the new .tar files for GUS
> >>and install from
> >>
> >> http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/GUS.tar.gz?cvsroot=GUS&f=h&tarball=1
> >>and from
> >>
> >> http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/install/install.tar.gz?cvsroot=GUS&f=h&tarball=1
> >>
> >>hopefully, that will fix your problem.  otherwise, let me know.
> >>
> >>steve
> >>
> >>Chetna Warade wrote:
> >>
> >>
> >>
> >>>Hi,
> >>>
> >>>Thanks for the mail,
> >>>
> >>>1) I am little confused here about the rehash and updateAllProjects
> >>>command.
> >>>Where does these two commands/plugins/scripts live. I mean are they
> >>>located in $GUS_HOME/bin directory..
> >>>
> >>>Also currently I haven't added the cvs on the $PROJECT/install and
> >>>$PROJECT/GUS directories but in other repository to keep track of
> >>>downloads at my side. So do you recommend putting it in $PROJECT install
> >>>and GUS directories.
> >>>
> >>>2) I am still getting this:
> >>>
> >>>[chetna@mango chetna]$ ga +meta --commit
> >>>Can't locate object method "userError" via package "GUS::Plugin
> >>>on" (perhaps you forgot to load "GUS::PluginMgr::GusApplication
> >>>home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> >>>[chetna@mango chetna]$
> >>>
> >>>Hope to hear from you
> >>>Chetna
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>$PROJECT_HOME contains the projects:  GUS, install, CBIL, etc.  GUS and
> >>>>install have CVS/ dirs, but CBIL doesn't because it is from the download
> >>>>site.
> >>>>
> >>>>steve
> >>>>
> >>>>Chetna Warade wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>Hi,
> >>>>>
> >>>>>I tried:
> >>>>>[chetna@mango chetna]$ ga +meta --commit
> >>>>>Can't locate object method "userError" via package
> >>>>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
> >>>>>"GUS::PluginMgr::GusApplication"?) at
> >>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> >>>>>[chetna@mango chetna]$
> >>>>>
> >>>>>Also to run cvs update do you expect a cvs system on the $PROJECT_HOME and
> >>>>>$GUS_HOME directories.
> >>>>>
> >>>>>I will send a test mail on the gusdev-gusdev-list,
> >>>>>
> >>>>>Thanks,
> >>>>>Chetna
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>>i don't think there are any resitrictions on who can write to the
> >>>>>>mailing list.  what address are you trying, and what happens?
> >>>>>>
> >>>>>>as far as ga is concerned, first, the command is ga +meta --commit (not
> >>>>>>--create).
> >>>>>>
> >>>>>>also, i think you should just make sure you have the latest.
> >>>>>>
> >>>>>>do this:
> >>>>>>1. get the latest CBIL download from:
> >>>>>>http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz
> >>>>>>2. cd $PROJECT_HOME/install
> >>>>>>     cvs update
> >>>>>>     rehash
> >>>>>>     updateAllProjects
> >>>>>>
> >>>>>>steve
> >>>>>>
> >>>>>>Chetna Warade wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>Hi,
> >>>>>>>
> >>>>>>>I am trying to mail to the mailing list and I am unable to do so. I am
> >>>>>>>wondering if I have enough permissions on the mail list.
> >>>>>>>
> >>>>>>>I am tyring to run:
> >>>>>>>
> >>>>>>>[chetna@mango chetna]$ ga +meta --create
> >>>>>>>Can't locate object method "userError" via package
> >>>>>>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
> >>>>>>>"GUS::PluginMgr::GusApplication"?) at
> >>>>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> >>>>>>>[chetna@mango chetna]$
> >>>>>>>
> >>>>>>>It would be great if you could help me debug this.
> >>>>>>>Thanks
> >>>>>>>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

[Gusdev-gusdev] Re: gusdev mailing list subscription

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

chetna-

1) can you send me the lines that you commented, so i can fix the problem.

2) the problem is that the tarball is excluding empty directories.  for 
now, create the following directories:

/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/SRes
/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/Core
/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/RAD3
/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/TESS

steve



Chetna Warade wrote:

>Hi Steve,
>
>1) I downloaded latest tars from cvsweb sanger and tried to "build GUS
>install -append". I remember reading about the rollback segments some
>weeks back but in my case I need to comment 3 lines from 
>$GUS_HOME/lib/perl/GUS/ObjRelP/ DbiDatabase.pm file.
>
>2)  But while building:
>.....
>     [copy] Copying 2 files to
>/home/projects/GUS/Model/src/java/org/gusdb/model/DoTS
>
>BUILD FAILED
>file:/home/projects/GUS/build.xml:123:
>/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/SRes not
>found.
>
>Because SRes is not there? Any idea I downloaded from cvsweb sanger today
>morning.
>
>Thanks for the help
>Chetna
>
>  
>
>>ok, i see how i confused you.  what i described works for folks that are 
>>using the cvs repository directly.
>>
>>in your case, instead, you should just get the new .tar files for GUS 
>>and install from
>>    
>> http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/GUS.tar.gz?cvsroot=GUS&f=h&tarball=1
>>and from
>>    
>> http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/install/install.tar.gz?cvsroot=GUS&f=h&tarball=1
>>
>>hopefully, that will fix your problem.  otherwise, let me know.
>>
>>steve
>>
>>Chetna Warade wrote:
>>
>>    
>>
>>>Hi,
>>>
>>>Thanks for the mail,
>>>
>>>1) I am little confused here about the rehash and updateAllProjects
>>>command.
>>>Where does these two commands/plugins/scripts live. I mean are they
>>>located in $GUS_HOME/bin directory..
>>>
>>>Also currently I haven't added the cvs on the $PROJECT/install and
>>>$PROJECT/GUS directories but in other repository to keep track of
>>>downloads at my side. So do you recommend putting it in $PROJECT install
>>>and GUS directories.
>>>
>>>2) I am still getting this:
>>>
>>>[chetna@mango chetna]$ ga +meta --commit
>>>Can't locate object method "userError" via package "GUS::Plugin
>>>on" (perhaps you forgot to load "GUS::PluginMgr::GusApplication
>>>home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
>>>[chetna@mango chetna]$
>>>
>>>Hope to hear from you
>>>Chetna
>>>
>>> 
>>>
>>>      
>>>
>>>>$PROJECT_HOME contains the projects:  GUS, install, CBIL, etc.  GUS and 
>>>>install have CVS/ dirs, but CBIL doesn't because it is from the download 
>>>>site.
>>>>
>>>>steve
>>>>
>>>>Chetna Warade wrote:
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>>>Hi,
>>>>>
>>>>>I tried:
>>>>>[chetna@mango chetna]$ ga +meta --commit
>>>>>Can't locate object method "userError" via package
>>>>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
>>>>>"GUS::PluginMgr::GusApplication"?) at
>>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
>>>>>[chetna@mango chetna]$
>>>>>
>>>>>Also to run cvs update do you expect a cvs system on the $PROJECT_HOME and
>>>>>$GUS_HOME directories.
>>>>>
>>>>>I will send a test mail on the gusdev-gusdev-list,
>>>>>
>>>>>Thanks,
>>>>>Chetna 
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>>>i don't think there are any resitrictions on who can write to the 
>>>>>>mailing list.  what address are you trying, and what happens?
>>>>>>
>>>>>>as far as ga is concerned, first, the command is ga +meta --commit (not 
>>>>>>--create).
>>>>>>
>>>>>>also, i think you should just make sure you have the latest.
>>>>>>
>>>>>>do this:
>>>>>>1. get the latest CBIL download from: 
>>>>>>http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz
>>>>>>2. cd $PROJECT_HOME/install
>>>>>>     cvs update
>>>>>>     rehash
>>>>>>     updateAllProjects
>>>>>>
>>>>>>steve
>>>>>>
>>>>>>Chetna Warade wrote:
>>>>>>
>>>>>>  
>>>>>>
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>Hi,
>>>>>>>
>>>>>>>I am trying to mail to the mailing list and I am unable to do so. I am
>>>>>>>wondering if I have enough permissions on the mail list.
>>>>>>>
>>>>>>>I am tyring to run:
>>>>>>>
>>>>>>>[chetna@mango chetna]$ ga +meta --create
>>>>>>>Can't locate object method "userError" via package
>>>>>>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
>>>>>>>"GUS::PluginMgr::GusApplication"?) at
>>>>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
>>>>>>>[chetna@mango chetna]$
>>>>>>>
>>>>>>>It would be great if you could help me debug this.
>>>>>>>Thanks
>>>>>>>Chetna 
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>    
>>>>>>>
>>>>>>>         
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>  
>>>>>>
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>   
>>>>
>>>>        
>>>>
>>> 
>>>
>>>      
>>>
>>    
>>
>
>
>  
>

[Gusdev-gusdev] Re: gusdev mailing list subscription

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

Hi Steve,

1) I downloaded latest tars from cvsweb sanger and tried to "build GUS
install -append". I remember reading about the rollback segments some
weeks back but in my case I need to comment 3 lines from 
$GUS_HOME/lib/perl/GUS/ObjRelP/ DbiDatabase.pm file.

2)  But while building:
.....
     [copy] Copying 2 files to
/home/projects/GUS/Model/src/java/org/gusdb/model/DoTS

BUILD FAILED
file:/home/projects/GUS/build.xml:123:
/home/projects/GUS/Model/src/java/org/gusdb/model/hand_edited/SRes not
found.

Because SRes is not there? Any idea I downloaded from cvsweb sanger today
morning.

Thanks for the help
Chetna

> ok, i see how i confused you.  what i described works for folks that are 
> using the cvs repository directly.
> 
> in your case, instead, you should just get the new .tar files for GUS 
> and install from
>     
>  http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/GUS.tar.gz?cvsroot=GUS&f=h&tarball=1
> and from
>     
>  http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/install/install.tar.gz?cvsroot=GUS&f=h&tarball=1
> 
> hopefully, that will fix your problem.  otherwise, let me know.
> 
> steve
> 
> Chetna Warade wrote:
> 
> >Hi,
> >
> >Thanks for the mail,
> >
> >1) I am little confused here about the rehash and updateAllProjects
> >command.
> >Where does these two commands/plugins/scripts live. I mean are they
> >located in $GUS_HOME/bin directory..
> >
> >Also currently I haven't added the cvs on the $PROJECT/install and
> >$PROJECT/GUS directories but in other repository to keep track of
> >downloads at my side. So do you recommend putting it in $PROJECT install
> >and GUS directories.
> >
> >2) I am still getting this:
> >
> >[chetna@mango chetna]$ ga +meta --commit
> >Can't locate object method "userError" via package "GUS::Plugin
> >on" (perhaps you forgot to load "GUS::PluginMgr::GusApplication
> >home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> >[chetna@mango chetna]$
> >
> >Hope to hear from you
> >Chetna
> >
> >  
> >
> >>$PROJECT_HOME contains the projects:  GUS, install, CBIL, etc.  GUS and 
> >>install have CVS/ dirs, but CBIL doesn't because it is from the download 
> >>site.
> >>
> >>steve
> >>
> >>Chetna Warade wrote:
> >>
> >>    
> >>
> >>>Hi,
> >>>
> >>>I tried:
> >>>[chetna@mango chetna]$ ga +meta --commit
> >>>Can't locate object method "userError" via package
> >>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
> >>>"GUS::PluginMgr::GusApplication"?) at
> >>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> >>>[chetna@mango chetna]$
> >>>
> >>>Also to run cvs update do you expect a cvs system on the $PROJECT_HOME and
> >>>$GUS_HOME directories.
> >>>
> >>>I will send a test mail on the gusdev-gusdev-list,
> >>>
> >>>Thanks,
> >>>Chetna 
> >>>
> >>> 
> >>>
> >>>      
> >>>
> >>>>i don't think there are any resitrictions on who can write to the 
> >>>>mailing list.  what address are you trying, and what happens?
> >>>>
> >>>>as far as ga is concerned, first, the command is ga +meta --commit (not 
> >>>>--create).
> >>>>
> >>>>also, i think you should just make sure you have the latest.
> >>>>
> >>>>do this:
> >>>> 1. get the latest CBIL download from: 
> >>>>http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz
> >>>> 2. cd $PROJECT_HOME/install
> >>>>      cvs update
> >>>>      rehash
> >>>>      updateAllProjects
> >>>>
> >>>>steve
> >>>>
> >>>>Chetna Warade wrote:
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>>>>Hi,
> >>>>>
> >>>>>I am trying to mail to the mailing list and I am unable to do so. I am
> >>>>>wondering if I have enough permissions on the mail list.
> >>>>>
> >>>>>I am tyring to run:
> >>>>>
> >>>>>[chetna@mango chetna]$ ga +meta --create
> >>>>>Can't locate object method "userError" via package
> >>>>>"GUS::PluginMgr::GusApplication" (perhaps you forgot to load
> >>>>>"GUS::PluginMgr::GusApplication"?) at
> >>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 44.
> >>>>>[chetna@mango chetna]$
> >>>>>
> >>>>>It would be great if you could help me debug this.
> >>>>>Thanks
> >>>>>Chetna 
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>     
> >>>>>
> >>>>>          
> >>>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>> 
> >>>
> >>>      
> >>>
> >>    
> >>
> >
> >
> >  
> >
> 
> 

[Gusdev-gusdev] updateAllProjects - helpful new command

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

folks-

i have added a new command to the build system.

it is:  updateAllProjects

it runs 'cvs update -d' on all directories in $PROJECT_HOME (that are 
from cvs).  In other words, it gets all your projects up to date (except 
if you have gotten CBIL from the download site).

to get it, do this:
  % cd $PROJECT_HOME/install
  % cvs update
  % rehash

then you should be able to run it like this:
  % updateAllProjects

In theory it is always safe to run this, because cvs update never 
clobbers your work.  but, it might merge in other people's work into 
files you are working on.

steve

[Gusdev-gusdev] plugin inventory

[Keith J. <kd...@sa...>]

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

-- 

- Keith James <kd...@sa...> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -