gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] Similarity table changes

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

Hi Jonathan,

Our databases are not really having any sequence overlap. So as you 
suggested the external_database_release_id should be fine. But when I look 
into the Dots.similarity and the dots.similarityspan I don't see anything 
pointing to externaldatabase/externaldatabaserelease. I was wondering if I 
missed out something or there is a linker.

Thanks

Sucheta

At 10:00 AM 7/19/2004 -0400, Jonathan Schug wrote:
>Sucheta, and All:
>
>If the blast libraries do not overlap, i.e., contain different sets of
>sequences, then there is probably no problem.  You can simply
>distinguish the Similarity rows by the target sequence's
>external_database_release_id.
>
>If the libraries overlap, then the issue is more difficult.  We don't
>have the notion of a library in this sense, and of course the library
>size affects the p-values for matches.  There is a DoTS::Library table
>that holds clone information that could be hacked to provide what you
>want, but I do *not* recommend it as a long term solution.  You could
>also use the DoTS::DbRefNaSequence or DoTS::AASequenceDbRef as
>appropriate to link to a DoTS::DbRef which links to an
>ExternalDatabase.  These tables could easily be used to gather
>sequences into multiple BLAST database files.
>
>The best solution is probably to create new tables.
>
>I propose, then the following changes to the Similarity table and the
>addition of new table to track search libraries:
>
>DoTS::Similarity
>   - add search_algorithm_invocation_id link to stably point to
>parameter values for the search.
>
>SRes::SearchLibrary
>   - contains a description of the search library including entry count
>etc.
>
>SRes::SearchLibraryMember
>   - uses a soft link, i.e., table_id, row_id to indicate membership.
>   - link is soft so that SearchLibrary can also be used for motifs,
>etc. that may not be in sequence table.
>   - SearchLibrary might contain a table_id to record what kind of
>entries are in the library.
>
>Thoughts?
>
>Jonathan
>
>On Jul 19, 2004, at 9:31 AM, Sucheta Tripathy wrote:
>
>>Hi Jonathan,
>>
>>Thanks for your reply. I also have a similar concern which I posted
>>sometimes back. My concern is to do with multiple databases rather
>>than the parameters for blast search. Currently we want to store blast
>>results against 23 different databases. Any suggestions which table
>>may be suitable?
>>
>>Thanks
>>
>>Sucheta
>>
>>At 12:18 AM 7/19/2004 -0400, Jonathan Schug wrote:
>>>Josef:
>>>
>>>The two columns in DoTS::Similarity that might be useful are algorithm
>>>and row_alg_invocation_id.  Algorithm is not recommended; it is meant
>>>to be used to distinguish, say, BLAST hits from FASTA hits.
>>>Row_alg_invocation_id is better and will work.  You can use the
>>>AlgoithmInvocation parameters.  However, this will not work if the
>>>rows
>>>are modified in some way later one.  Later updates will change the
>>>row_alg_invocation_id ruining this scheme.  You could also consider
>>>linking Similarity rows to the invocation via an Evidence row.  This
>>>is
>>>more stable.
>>>
>>>PlasmoDB faced this when tuning BLAST parameters to avoid the problems
>>>with the high AT content of the Pf genome.  They may have tuned the
>>>parameters outside of the DB.
>>>
>>>You might also consider running the BLAST searches with the most
>>>lenient parameters, then recreating the more stringent searches with
>>>query parameters if this is possible
>>>
>>>Jonathan
>>>
>>>
>>>---------------------------------------------------------------------- 
>>>-- ---
>>>Jonathan Schug            Center for Bioinformatics
>>>js...@pc...     Computational Biology and Informatics Lab
>>>(215) 573-3113 voice      University of Pennsylvania,
>>>(215) 573-3111 fax        1413 Blockley Hall, Philadelphia, PA
>>>19014-6021
>>>
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by BEA Weblogic Workshop
>>>FREE Java Enterprise J2EE developer tools!
>>>Get your free copy of BEA WebLogic Workshop 8.1 today.
>>>http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>-------------------------------------------------------
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>FREE Java Enterprise J2EE developer tools!
>Get your free copy of BEA WebLogic Workshop 8.1 today.
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>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] RIVList

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

Hey Paul,

Sorry, this is a result of someone checking in code that doesn't compile. 
This is an example of where the -skipJavaCompiling option would be useful. 
However, if there is other java code in the GUS project that you actually 
do want to use, I would suggest simply removing the GUS/WebDevKit 
component (cd {Project_Home}/GUS; rm -r WebDevKit), assuming you're not 
using that for any reason.

Dave


If you are not using the GUS WebDevKit component, I would suggest

On Mon, 19 Jul 2004, Paul Mooney wrote:

> HI,
>
> I did a `cvs update -dP` then `build GUS install --append`
> I got the following error - does somebody need to commit a file?
>
>    [javac] Since fork is true, ignoring compiler setting.
>    [javac] Compiling 59 source files to 
> /nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/classes
>    [javac] Since fork is true, ignoring compiler setting.
>    [javac] 
> /nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/src/java/org/gusdb/gus/wdk/ 
> controller/servlets/InteractiveRecordListServlet.java:13: cannot resolve 
> symbol
>    [javac] symbol  : class RIVList
>    [javac] location: package view
>    [javac] import org.gusdb.gus.wdk.view.RIVList;
>    [javac]                               ^
>    [javac] 
> /nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/src/java/org/gusdb/gus/wdk/ 
> controller/servlets/InteractiveRecordListServlet.java:177: cannot resolve 
> symbol
>    [javac] symbol  : class RIVList
>    [javac] location: class 
> org.gusdb.gus.wdk.controller.servlets.InteractiveRecordListServlet
>    [javac]             RIVList rivl = new RIVList(si);
>    [javac]             ^
>    [javac] 
> /nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/src/java/org/gusdb/gus/wdk/ 
> controller/servlets/InteractiveRecordListServlet.java:177: cannot resolve 
> symbol
>    [javac] symbol  : class RIVList
>    [javac] location: class 
> org.gusdb.gus.wdk.controller.servlets.InteractiveRecordListServlet
>    [javac]             RIVList rivl = new RIVList(si);
>    [javac]                                ^
>    [javac] 3 errors
>
>
>
> -------------------------------------------------------
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> FREE Java Enterprise J2EE developer tools!
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>

[Gusdev-gusdev] Similarity table changes

[Jonathan S. <js...@pc...>]

Sucheta, and All:

If the blast libraries do not overlap, i.e., contain different sets of  
sequences, then there is probably no problem.  You can simply  
distinguish the Similarity rows by the target sequence's  
external_database_release_id.

If the libraries overlap, then the issue is more difficult.  We don't  
have the notion of a library in this sense, and of course the library  
size affects the p-values for matches.  There is a DoTS::Library table  
that holds clone information that could be hacked to provide what you  
want, but I do *not* recommend it as a long term solution.  You could  
also use the DoTS::DbRefNaSequence or DoTS::AASequenceDbRef as  
appropriate to link to a DoTS::DbRef which links to an  
ExternalDatabase.  These tables could easily be used to gather  
sequences into multiple BLAST database files.

The best solution is probably to create new tables.

I propose, then the following changes to the Similarity table and the  
addition of new table to track search libraries:

DoTS::Similarity
   - add search_algorithm_invocation_id link to stably point to  
parameter values for the search.

SRes::SearchLibrary
   - contains a description of the search library including entry count  
etc.

SRes::SearchLibraryMember
   - uses a soft link, i.e., table_id, row_id to indicate membership.
   - link is soft so that SearchLibrary can also be used for motifs,  
etc. that may not be in sequence table.
   - SearchLibrary might contain a table_id to record what kind of  
entries are in the library.

Thoughts?

Jonathan

On Jul 19, 2004, at 9:31 AM, Sucheta Tripathy wrote:

> Hi Jonathan,
>
> Thanks for your reply. I also have a similar concern which I posted  
> sometimes back. My concern is to do with multiple databases rather  
> than the parameters for blast search. Currently we want to store blast  
> results against 23 different databases. Any suggestions which table  
> may be suitable?
>
> Thanks
>
> Sucheta
>
> At 12:18 AM 7/19/2004 -0400, Jonathan Schug wrote:
>> Josef:
>>
>> The two columns in DoTS::Similarity that might be useful are algorithm
>> and row_alg_invocation_id.  Algorithm is not recommended; it is meant
>> to be used to distinguish, say, BLAST hits from FASTA hits.
>> Row_alg_invocation_id is better and will work.  You can use the
>> AlgoithmInvocation parameters.  However, this will not work if the  
>> rows
>> are modified in some way later one.  Later updates will change the
>> row_alg_invocation_id ruining this scheme.  You could also consider
>> linking Similarity rows to the invocation via an Evidence row.  This  
>> is
>> more stable.
>>
>> PlasmoDB faced this when tuning BLAST parameters to avoid the problems
>> with the high AT content of the Pf genome.  They may have tuned the
>> parameters outside of the DB.
>>
>> You might also consider running the BLAST searches with the most
>> lenient parameters, then recreating the more stringent searches with
>> query parameters if this is possible
>>
>> Jonathan
>>
>>
>> ---------------------------------------------------------------------- 
>> -- ---
>> Jonathan Schug            Center for Bioinformatics
>> js...@pc...     Computational Biology and Informatics Lab
>> (215) 573-3113 voice      University of Pennsylvania,
>> (215) 573-3111 fax        1413 Blockley Hall, Philadelphia, PA
>> 19014-6021
>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by BEA Weblogic Workshop
>> FREE Java Enterprise J2EE developer tools!
>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Multiple blast analyses - few options

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

Hi Jonathan,

Thanks for your reply. I also have a similar concern which I posted 
sometimes back. My concern is to do with multiple databases rather than the 
parameters for blast search. Currently we want to store blast results 
against 23 different databases. Any suggestions which table may be suitable?

Thanks

Sucheta

At 12:18 AM 7/19/2004 -0400, Jonathan Schug wrote:
>Josef:
>
>The two columns in DoTS::Similarity that might be useful are algorithm
>and row_alg_invocation_id.  Algorithm is not recommended; it is meant
>to be used to distinguish, say, BLAST hits from FASTA hits.
>Row_alg_invocation_id is better and will work.  You can use the
>AlgoithmInvocation parameters.  However, this will not work if the rows
>are modified in some way later one.  Later updates will change the
>row_alg_invocation_id ruining this scheme.  You could also consider
>linking Similarity rows to the invocation via an Evidence row.  This is
>more stable.
>
>PlasmoDB faced this when tuning BLAST parameters to avoid the problems
>with the high AT content of the Pf genome.  They may have tuned the
>parameters outside of the DB.
>
>You might also consider running the BLAST searches with the most
>lenient parameters, then recreating the more stringent searches with
>query parameters if this is possible
>
>Jonathan
>
>
>------------------------------------------------------------------------ ---
>Jonathan Schug            Center for Bioinformatics
>js...@pc...     Computational Biology and Informatics Lab
>(215) 573-3113 voice      University of Pennsylvania,
>(215) 573-3111 fax        1413 Blockley Hall, Philadelphia, PA
>19014-6021
>
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by BEA Weblogic Workshop
>FREE Java Enterprise J2EE developer tools!
>Get your free copy of BEA WebLogic Workshop 8.1 today.
>http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] RIVList

[Paul M. <pj...@sa...>]

HI,

I did a `cvs update -dP` then `build GUS install --append`
I got the following error - does somebody need to commit a file?

     [javac] Since fork is true, ignoring compiler setting.
     [javac] Compiling 59 source files to  
/nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/classes
     [javac] Since fork is true, ignoring compiler setting.
     [javac]  
/nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/src/java/org/gusdb/gus/wdk/ 
controller/servlets/InteractiveRecordListServlet.java:13: cannot  
resolve symbol
     [javac] symbol  : class RIVList
     [javac] location: package view
     [javac] import org.gusdb.gus.wdk.view.RIVList;
     [javac]                               ^
     [javac]  
/nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/src/java/org/gusdb/gus/wdk/ 
controller/servlets/InteractiveRecordListServlet.java:177: cannot  
resolve symbol
     [javac] symbol  : class RIVList
     [javac] location: class  
org.gusdb.gus.wdk.controller.servlets.InteractiveRecordListServlet
     [javac]             RIVList rivl = new RIVList(si);
     [javac]             ^
     [javac]  
/nfs/team81/pjm/CVS/CVS-new/GUS/WebDevKit/src/java/org/gusdb/gus/wdk/ 
controller/servlets/InteractiveRecordListServlet.java:177: cannot  
resolve symbol
     [javac] symbol  : class RIVList
     [javac] location: class  
org.gusdb.gus.wdk.controller.servlets.InteractiveRecordListServlet
     [javac]             RIVList rivl = new RIVList(si);
     [javac]                                ^
     [javac] 3 errors

[Gusdev-gusdev] Multiple blast analyses - few options

[Jonathan S. <js...@pc...>]

Josef:

The two columns in DoTS::Similarity that might be useful are algorithm  
and row_alg_invocation_id.  Algorithm is not recommended; it is meant  
to be used to distinguish, say, BLAST hits from FASTA hits.   
Row_alg_invocation_id is better and will work.  You can use the  
AlgoithmInvocation parameters.  However, this will not work if the rows  
are modified in some way later one.  Later updates will change the  
row_alg_invocation_id ruining this scheme.  You could also consider  
linking Similarity rows to the invocation via an Evidence row.  This is  
more stable.

PlasmoDB faced this when tuning BLAST parameters to avoid the problems  
with the high AT content of the Pf genome.  They may have tuned the  
parameters outside of the DB.

You might also consider running the BLAST searches with the most  
lenient parameters, then recreating the more stringent searches with  
query parameters if this is possible

Jonathan


------------------------------------------------------------------------ 
---
Jonathan Schug            Center for Bioinformatics
js...@pc...     Computational Biology and Informatics Lab
(215) 573-3113 voice      University of Pennsylvania,
(215) 573-3111 fax        1413 Blockley Hall, Philadelphia, PA  
19014-6021

[Gusdev-gusdev] Multiple blast analyses

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

How might one deposit multiple blast analyses
(different blast parameters) which use the same subject
and query sequence into DoTS.Similarity/DoTS.SimilaritySpan
so that one can distinguish between these two analyses?

Thank, Josef


Josef Jurek

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

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

Re: [Gusdev-gusdev] insufficient privileges on Core.Algorithm_SQ sequence

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

Hi Juan,

I'd be slightly careful with this approach to GUS permissions--  as 
you've pointed out, you've effectively made GUSrw a pseudo-dba, who may 
manipulate any table-- public or private-- in the entire instance.  I 
believe this also includes Oracle schemas, which is probably a pretty 
significant security risk.

Here at CBIL, we've eliminated the GUSrw and GUSdevReadOnly accounts, 
choosing to use a combination of individual accounts, and roles.  In 
this fashion, we grant (using the grantPermissions script, or custom 
PL/SQL scripts) SELECT, INSERT, UPDATE, DELETE on all tables, views, 
materialized views, and sequences (as appropriate) in the GUS schemas.  
We also grant REFERENCES as appropriate.  These grants are against the 
roles, the roles are then granted to the users.  We have a GUS_R (gus 
read) role, and a gus write role.

One word of note:  There are certain privileges which cannot be granted 
via roles.

--Mike

On Jul 16, 2004, at 2:23 PM, Juan Perin wrote:

>> --This is to grant permission to the users
>>
>> GRANT CREATE SESSION TO GUSrw;
>> GRANT CREATE TABLE TO GUSrw;
>> GRANT CREATE VIEW TO GUSrw;
>> GRANT CREATE SEQUENCE TO GUSrw;
>> GRANT CREATE TRIGGER TO GUSrw;
>> GRANT CREATE SYNONYM TO GUSrw;
>> GRANT SELECT ANY TABLE TO GUSrw;
>> GRANT INSERT ANY TABLE TO GUSrw;
>> GRANT UPDATE ANY TABLE TO GUSrw;
>> GRANT DELETE ANY TABLE TO GUSrw;
>> GRANT CREATE SESSION TO GUSdevReadOnly;
>> GRANT SELECT ANY TABLE TO GUSdevReadOnly;
>> GRANT SELECT ANY TABLE TO GUSdevReadOnly;
>> --------------------------------------------------
>
> To the above list, we had to add the line:
>
> GRANT SELECT ANY SEQUENCE TO GUSrw;
>
> After doing this, the "ga +meta --commit" command worked properly.
>
> Should this have been necessary?  Are other people just making GUSrw 
> into a
> DBA or something to get around this?
>
> Thanks,
> Juan & Kevin
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] insufficient privileges on Core.Algorithm_SQ sequence

[Juan P. <BI...@ge...>]

> --This is to grant permission to the users
> 
> GRANT CREATE SESSION TO GUSrw;
> GRANT CREATE TABLE TO GUSrw;
> GRANT CREATE VIEW TO GUSrw;
> GRANT CREATE SEQUENCE TO GUSrw;
> GRANT CREATE TRIGGER TO GUSrw;
> GRANT CREATE SYNONYM TO GUSrw;
> GRANT SELECT ANY TABLE TO GUSrw;
> GRANT INSERT ANY TABLE TO GUSrw;
> GRANT UPDATE ANY TABLE TO GUSrw;
> GRANT DELETE ANY TABLE TO GUSrw;
> GRANT CREATE SESSION TO GUSdevReadOnly;
> GRANT SELECT ANY TABLE TO GUSdevReadOnly;
> GRANT SELECT ANY TABLE TO GUSdevReadOnly;
> --------------------------------------------------

To the above list, we had to add the line:

GRANT SELECT ANY SEQUENCE TO GUSrw;

After doing this, the "ga +meta --commit" command worked properly.

Should this have been necessary?  Are other people just making GUSrw into a
DBA or something to get around this?

Thanks,
Juan & Kevin

Re: [Gusdev-gusdev] insufficient privileges on Core.Algorithm_SQ sequence

[Pablo N. M. <pa...@pa...>]

Hi Kevin and Juan,
I don't know what could have caused this error, but I would try one of
these (or both):

Run the grantPermissions script ($GUS_HOME/bin/grantPermissions.pl) or
recreate the users (I used the create-gus-users.sql shown below).

[create-gus-users.sql]
--------------------------------------------------
--This is to create the users.
DROP USER GUSRW CASCADE;
CREATE USER GUSRW IDENTIFIED BY <password> TEMPORARY TABLESPACE TEMP
DEFAULT TABLESPACE users QUOTA UNLIMITED ON TEMP QUOTA UNLIMITED ON
users;

DROP USER GUSdevReadOnly CASCADE;
CREATE USER GUSdevReadOnly IDENTIFIED BY <password> TEMPORARY TABLESPACE
TEMP DEFAULT TABLESPACE users QUOTA UNLIMITED ON TEMP QUOTA UNLIMITED ON
users;

--This is to grant permission to the users

GRANT CREATE SESSION TO GUSrw;
GRANT CREATE TABLE TO GUSrw;
GRANT CREATE VIEW TO GUSrw;
GRANT CREATE SEQUENCE TO GUSrw;
GRANT CREATE TRIGGER TO GUSrw;
GRANT CREATE SYNONYM TO GUSrw;
GRANT SELECT ANY TABLE TO GUSrw;
GRANT INSERT ANY TABLE TO GUSrw;
GRANT UPDATE ANY TABLE TO GUSrw;
GRANT DELETE ANY TABLE TO GUSrw;
GRANT CREATE SESSION TO GUSdevReadOnly;
GRANT SELECT ANY TABLE TO GUSdevReadOnly;
GRANT SELECT ANY TABLE TO GUSdevReadOnly;
--------------------------------------------------

Best wishes,
Pablo

-- 
-----------------------------
Pablo Nascimento Mendes
Research Scholar
Kissinger Lab
Department of Genetics
University of Georgia
C210 Life Sciences Bldg.
Athens, Georgia 30602
Phone:706 542-1447
E-mail: pa...@ug...


On Thu, 2004-07-15 at 18:52, Kevin Murphy wrote:
> Hi gusdev-gusdev list,
> 
> (I'm working on the same installation with Juan Perin, who has posted a  
> couple times in the last few days).
> 
> While following the VBI PDF guide to GUS installation, we've  
> encountered an error at the following step:
> 
> ga +meta --commit
> 
> After writing the </Core::Algorithm> tag (see full output below), there  
> is an error, apparently because the user does not have sufficient  
> privileges on the Core.Algorithm_SQ sequence.
> 
> I inserted a debug statement to look at DBH->{Username}, and it is  
> GUSrw.  Using sqlplus shows that GUSrw can't read this sequence, but  
> the sequence does exist in ALL_SEQUENCES.
> 
> What do you think has gone wrong with our installation?  We've been  
> guilty of some errors along the way (typos in config files, use of  
> vbi's properties file instead of deriving from the sample, etc) and had  
> to run the 'build' script a number of times.  Is it brittle?
> 
> Thanks,
> Kevin Murphy
> 
> - - - -
> 
> [gus@rad GUS]$ ga +meta --commit
>    <Core::Algorithm>
>      <name>GA-Plugin</name>
>      <description>GUS application framework for plugins</description>
>      <Core::AlgorithmImplementation>
>        <cvs_revision>1.49</cvs_revision>
>        <cvs_tag> </cvs_tag>
>        <executable>GUS::PluginMgr::GusApplication</executable>
>        <executable_md5>e291775acbf95c5ed6bae9024ad78e79</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::db prepare failed: ORA-01031: insufficient privileges (DBD  
> ERROR: error possibly near <*> indicator at char 12 in 's\
> elect Core.<*>Algorithm_SQ.NEXTVAL from DUAL') [for Statement "select  
> Core.Algorithm_SQ.NEXTVAL from DUAL"] at /checkout/GUS/lib/\
> perl/GUS/ObjRelP/DbiTable.pm line 551.
> Failed preparing sql 'select Core.Algorithm_SQ.NEXTVAL from DUAL' with  
> error: ORA-01031: insufficient privileges (DBD ERROR: erro\
> r possibly near <*> indicator at char 12 in 'select  
> Core.<*>Algorithm_SQ.NEXTVAL from DUAL') at  
> /checkout/GUS/lib/perl/GUS/ObjRel\
> P/DbiTable.pm line 551
>           
> GUS::ObjRelP::DbiTable::getNextID('GUS::Model::Core:: 
> Algorithm_Table=HASH(0x86b2560)', undef) called at /checkout/GUS/lib\
> /perl/GUS/ObjRelP/DbiRow.pm line 535
>           
> GUS::ObjRelP::DbiRow::getNextID('GUS::Model::Core:: 
> Algorithm=HASH(0x86591d0)') called at /checkout/GUS/lib/perl/GUS/ObjRe\
> lP/DbiRow.pm line 606
>           
> GUS::ObjRelP::DbiRow::insert('GUS::Model::Core:: 
> Algorithm=HASH(0x86591d0)') called at  
> /checkout/GUS/lib/perl/GUS/Model/Gu\
> sRow.pm line 1677
>           
> GUS::Model::GusRow::submit('GUS::Model::Core:: 
> Algorithm=HASH(0x86591d0)') called at  
> /checkout/GUS/lib/perl/GUS/PluginMgr/\
> GusApplication.pm line 355
>           
> GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbc2c)', undef) called at /chec\
> kout/GUS/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>           
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbc2c)', undef) called at /checkout/\
> GUS/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>           
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbc2c)', 'ARRAY(0x81049d0)') called \
> at /checkout/GUS/bin/ga line 11
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
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[Gusdev-gusdev] Creating Tables and new GUS

[Juan P. <BI...@ge...>]

Just a heads-up to anyone building GUS from the tutorials listed at
gusdb.org.  (Specifically in the VBIdoc.pdf).  If you use the
'create_tables.sql' that is given as an example you must add the tablespace
creation lines as specified below in order to build GUS appropriately.

Hopefully this addition is enough to acknowledge

create tablespace gus_app
datafile '/oracle/gus/dynmgus_app.dbf' size 200M
autoextend on next 10M maxsize 5000M
default storage (initial 4M next 1M pctincrease 0);
create tablespace gus_app_idx
datafile '/oracle/gus/dynmgus_app_idx.dbf' size 200M
autoextend on next 10M maxsize 5000M
default storage (initial 4M next 1M pctincrease 0);

[Gusdev-gusdev] insufficient privileges on Core.Algorithm_SQ sequence

[Kevin M. <mu...@ge...>]

Hi gusdev-gusdev list,

(I'm working on the same installation with Juan Perin, who has posted a  
couple times in the last few days).

While following the VBI PDF guide to GUS installation, we've  
encountered an error at the following step:

ga +meta --commit

After writing the </Core::Algorithm> tag (see full output below), there  
is an error, apparently because the user does not have sufficient  
privileges on the Core.Algorithm_SQ sequence.

I inserted a debug statement to look at DBH->{Username}, and it is  
GUSrw.  Using sqlplus shows that GUSrw can't read this sequence, but  
the sequence does exist in ALL_SEQUENCES.

What do you think has gone wrong with our installation?  We've been  
guilty of some errors along the way (typos in config files, use of  
vbi's properties file instead of deriving from the sample, etc) and had  
to run the 'build' script a number of times.  Is it brittle?

Thanks,
Kevin Murphy

- - - -

[gus@rad GUS]$ ga +meta --commit
   <Core::Algorithm>
     <name>GA-Plugin</name>
     <description>GUS application framework for plugins</description>
     <Core::AlgorithmImplementation>
       <cvs_revision>1.49</cvs_revision>
       <cvs_tag> </cvs_tag>
       <executable>GUS::PluginMgr::GusApplication</executable>
       <executable_md5>e291775acbf95c5ed6bae9024ad78e79</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::db prepare failed: ORA-01031: insufficient privileges (DBD  
ERROR: error possibly near <*> indicator at char 12 in 's\
elect Core.<*>Algorithm_SQ.NEXTVAL from DUAL') [for Statement "select  
Core.Algorithm_SQ.NEXTVAL from DUAL"] at /checkout/GUS/lib/\
perl/GUS/ObjRelP/DbiTable.pm line 551.
Failed preparing sql 'select Core.Algorithm_SQ.NEXTVAL from DUAL' with  
error: ORA-01031: insufficient privileges (DBD ERROR: erro\
r possibly near <*> indicator at char 12 in 'select  
Core.<*>Algorithm_SQ.NEXTVAL from DUAL') at  
/checkout/GUS/lib/perl/GUS/ObjRel\
P/DbiTable.pm line 551
          
GUS::ObjRelP::DbiTable::getNextID('GUS::Model::Core:: 
Algorithm_Table=HASH(0x86b2560)', undef) called at /checkout/GUS/lib\
/perl/GUS/ObjRelP/DbiRow.pm line 535
          
GUS::ObjRelP::DbiRow::getNextID('GUS::Model::Core:: 
Algorithm=HASH(0x86591d0)') called at /checkout/GUS/lib/perl/GUS/ObjRe\
lP/DbiRow.pm line 606
          
GUS::ObjRelP::DbiRow::insert('GUS::Model::Core:: 
Algorithm=HASH(0x86591d0)') called at  
/checkout/GUS/lib/perl/GUS/Model/Gu\
sRow.pm line 1677
          
GUS::Model::GusRow::submit('GUS::Model::Core:: 
Algorithm=HASH(0x86591d0)') called at  
/checkout/GUS/lib/perl/GUS/PluginMgr/\
GusApplication.pm line 355
          
GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr:: 
GusApplication=HASH(0x80fbc2c)', undef) called at /chec\
kout/GUS/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
          
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr:: 
GusApplication=HASH(0x80fbc2c)', undef) called at /checkout/\
GUS/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
          
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr:: 
GusApplication=HASH(0x80fbc2c)', 'ARRAY(0x81049d0)') called \
at /checkout/GUS/bin/ga line 11

Re: [Gusdev-gusdev] Building GUS on a previous installation

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

Thanks Pablo,

I have infact rebuild the objects and did not see any anomalies so far
with the data, and not even to the sequences. The only weirdness I
observed was the important plugin GBParser stopped functioning, but I
fixed it, so things are OK now. I have not however tried with the updated
version of the source from the cvs.

One thing I may like to ask the forum is in case you build an older
version of GUS it asks you to update the plugin with

GUS +update ...

But when you do update it says its already registered. I have adopted a
method which seems not the right way to do. I simply change the CVS
version and do an update.

I will appreciate if any one can answer an elegant way to do this.

Thanks

Sucheta

> Hi Sucheta,
> I apologize for the delay on responding to you. I'll try to give you the
> best of my short knowledge on GUS up to now. Most of this you probably
> already know.
>
> The installation shouldn't touch the data at all. However, we had all
> the oracle sequences in the database reset to 1 the first time we tried
> to rebuild GUS. The installation seems to be fixed now, as long as we've
> ran it again with no problem.
>
> All the database-related installation seems to be performed separately
> (for example the create-db.sh script). Looks like the build just
> generates the object layer.
>
> Probably the only way to make sure is to take a look at the Ant tasks
> (build.xml), but I just wanted to let you know that we've not observed
> any abnormality up to now.
>
> Besides the table creation itself, you will probably want to create an
> oracle sequence to handle the primary key auto increment. Then you'll
> need rerun the grantPermissions.pl script to give you rights to access
> the recently created stuff.
>
> Best regards,
> Pablo
>
> On Thu, 2004-07-08 at 12:26, Sucheta Tripathy wrote:
>> Hi Steve, Michael,
>>
>> I know there were a lots of discussion on this earlier where Michael had
>> created some new tables. However, I am not clear what happens to the
>> data
>> if you build GUS on a previous installtion.
>>
>> The reason I ask this is with the earlier distribution we don't have the
>> dots.scaffoldgapfeature view and I want to create this. I saw the
>> detailed
>> instruction on this in wiki page, just wanted to make sure the existing
>> data in the tables can be restored.
>>
>> Thanks
>>
>> Sucheta
>
> --
> -----------------------------
> Pablo Nascimento Mendes
> Research Scholar
> Kissinger Lab
> Department of Genetics
> University of Georgia
> C210 Life Sciences Bldg.
> Athens, Georgia 30602
> Phone:706 542-1447
> E-mail: pa...@ug...
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
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> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] Building GUS on a previous installation

[Pablo N. M. <pa...@pa...>]

Hi Sucheta,
I apologize for the delay on responding to you. I'll try to give you the
best of my short knowledge on GUS up to now. Most of this you probably
already know.

The installation shouldn't touch the data at all. However, we had all
the oracle sequences in the database reset to 1 the first time we tried
to rebuild GUS. The installation seems to be fixed now, as long as we've
ran it again with no problem.

All the database-related installation seems to be performed separately
(for example the create-db.sh script). Looks like the build just
generates the object layer.

Probably the only way to make sure is to take a look at the Ant tasks
(build.xml), but I just wanted to let you know that we've not observed
any abnormality up to now.

Besides the table creation itself, you will probably want to create an
oracle sequence to handle the primary key auto increment. Then you'll
need rerun the grantPermissions.pl script to give you rights to access
the recently created stuff.

Best regards,
Pablo

On Thu, 2004-07-08 at 12:26, Sucheta Tripathy wrote:
> Hi Steve, Michael,
> 
> I know there were a lots of discussion on this earlier where Michael had 
> created some new tables. However, I am not clear what happens to the data 
> if you build GUS on a previous installtion.
> 
> The reason I ask this is with the earlier distribution we don't have the 
> dots.scaffoldgapfeature view and I want to create this. I saw the detailed 
> instruction on this in wiki page, just wanted to make sure the existing 
> data in the tables can be restored.
> 
> Thanks
> 
> Sucheta

-- 
-----------------------------
Pablo Nascimento Mendes
Research Scholar
Kissinger Lab
Department of Genetics
University of Georgia
C210 Life Sciences Bldg.
Athens, Georgia 30602
Phone:706 542-1447
E-mail: pa...@ug...

Re: [Gusdev-gusdev] Go annotation upload

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

Yes if you do a cvs update in the GUS/GOPredict component, you should be 
able to rebuild.  That would probably be the easiest way.

I believe you will also need the latest release of the CBIL project. 
Download "CBIL_v1-5-0.tar.gz" from

http://www.cbil.upenn.edu/downloads/CBIL/releases/

and replace your existing CBIL directory in {PROJECT_HOME} with the 1.5 
version (assuming you haven't updated that recently).

Dave


On Thu, 15 Jul 2004, Thomas Otto wrote:

> Hi Dave,
>
> when I do not have this plugin in my GUS directory, can I download it over 
> the cvs and then rebuild the stuff, or can you just send it to me? I think 
> there are some modules missing in my build, done last december...
>
> Thanks,
> Thomas
>
> Dave Barkan wrote:
>
>> Whoops, that last message was a mistake on my part, I read the email too 
>> fast.
>> 
>> Try GUS::GOPredict::Plugin::LoadGoAssociation.  This is pretty well 
>> documented as well.  In addition to loading the annotations (in the 
>> DoTS.GOAssociation table) loads data into some other tables that we use 
>> for our CBIL GO Predictor, but you might not need (mostly the table 
>> DoTS.GOAssociationInstance).  Give it a whirl and let me know how it goes.
>> 
>> Dave
>> 
>> On Thu, 15 Jul 2004, Thomas Otto wrote:
>> 
>>> Hello -,
>>> 
>>> with witch plugin can I upload the Goannotations from the 
>>> http://www.geneontology.org/GO.current.annotations.shtml page?
>>> 
>>> Thanks in advance,
>>> 
>>> Thomas
>>> 
>>> 
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>> FREE Java Enterprise J2EE developer tools!
>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
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>>> _______________________________________________
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>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> 
>> 
>> 
>> -------------------------------------------------------
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>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> 
>

Re: [Gusdev-gusdev] Go annotation upload

[Thomas O. <ot...@fi...>]

Hi Dave,

when I do not have this plugin in my GUS directory, can I download it 
over the cvs and then rebuild the stuff, or can you just send it to me? 
I think there are some modules missing in my build, done last december...

Thanks,
Thomas

Dave Barkan wrote:

> Whoops, that last message was a mistake on my part, I read the email 
> too fast.
>
> Try GUS::GOPredict::Plugin::LoadGoAssociation.  This is pretty well 
> documented as well.  In addition to loading the annotations (in the 
> DoTS.GOAssociation table) loads data into some other tables that we 
> use for our CBIL GO Predictor, but you might not need (mostly the 
> table DoTS.GOAssociationInstance).  Give it a whirl and let me know 
> how it goes.
>
> Dave
>
> On Thu, 15 Jul 2004, Thomas Otto wrote:
>
>> Hello -,
>>
>> with witch plugin can I upload the Goannotations from the 
>> http://www.geneontology.org/GO.current.annotations.shtml page?
>>
>> Thanks in advance,
>>
>> Thomas
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by BEA Weblogic Workshop
>> FREE Java Enterprise J2EE developer tools!
>> Get your free copy of BEA WebLogic Workshop 8.1 today.
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>> _______________________________________________
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>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
> -------------------------------------------------------
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>

Re: [Gusdev-gusdev] Go annotation upload

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

Whoops, that last message was a mistake on my part, I read the email too 
fast.

Try GUS::GOPredict::Plugin::LoadGoAssociation.  This is pretty well 
documented as well.  In addition to loading the annotations (in the 
DoTS.GOAssociation table) loads data into some other tables that we use 
for our CBIL GO Predictor, but you might not need (mostly the table 
DoTS.GOAssociationInstance).  Give it a whirl and let me know how it goes.

Dave

On Thu, 15 Jul 2004, Thomas Otto wrote:

> Hello -,
>
> with witch plugin can I upload the Goannotations from the 
> http://www.geneontology.org/GO.current.annotations.shtml page?
>
> Thanks in advance,
>
> Thomas
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] Go annotation upload

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

try GUS::GOPredict::Plugin::LoadGoOntology.  It should be pretty well 
documented, but let me know if you have any questions.

Dave

On Thu, 15 Jul 2004, Thomas Otto wrote:

> Hello -,
>
> with witch plugin can I upload the Goannotations from the 
> http://www.geneontology.org/GO.current.annotations.shtml page?
>
> Thanks in advance,
>
> Thomas
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] Go annotation upload

[Thomas O. <ot...@fi...>]

Hello -,

with witch plugin can I upload the Goannotations from the 
http://www.geneontology.org/GO.current.annotations.shtml page?

Thanks in advance,

Thomas

Re: [Gusdev-gusdev] LoadBlastSimFast.pm

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

Hi Pablo,

We were seeing errors like this a couple days ago and made our own 
changes.  I have a feeling your Oracle.pm module might not be up-to-date 
with regards to the CVS repository because one thing we did was rename the 
nextValVar method in Oracle.pm!  I would recommend the following steps 
(all surface-level changes but will make things easier for you in the 
future):

1. cvs update Oracle.pm

2. change line 435 in LoadBlastSimFast so the method name is "nextVal", 
not "nextValVar".

I will change it similarly and commit to CVS (so I guess alternatively you 
could just cvs update LoadBlastSimFast when I'm done, although I think you 
would have to resolve conflicts.)

Your message is definitely standard procedure; thanks for bringing it to 
our attention!

Dave

  On Tue, 13 Jul 2004, Pablo Nascimento Mendes wrote:

> Hello dev folks,
> I was getting errors when running the LoadBlastSimFast plug-in. It seems
> to be due to an update in the Oracle.pm.
>
> Error msg:
> Can't locate object method "nextValSql" via package
> "GUS::ObjRelP::Oracle" (perhaps you forgot to load
> "GUS::ObjRelP::Oracle"?) at
> /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm line
> 435, <GEN0> line 1654.
>
> I found this line in the LoadBlastSimFast.pm
> 433:  my $nextvalSql =
> $db->getDbPlatform()->nextValSql("dots.SimilaritySpan");
>
> Then I changed to:
> my $nextvalSql =
> $db->getDbPlatform()->nextValVar("dots.SimilaritySpan");
>
> Now it's working fine.
>
> I don't know what is the standard procedure, but I'm reporting the error
> so somebody with "The Power" :) who can fix and commit the changes to
> the CVS.
>
> Please let me know if there is a better way to proceed in cases like
> this.
>
> Best regards,
> Pablo
> --
> -----------------------------
> Pablo Nascimento Mendes
> Research Scholar
> Kissinger Lab
> Department of Genetics
> University of Georgia
> C210 Life Sciences Bldg.
> Athens, Georgia 30602
> Phone:706 542-1447
> E-mail: pa...@ug...
>
>
>
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 -
> digital self defense, top technical experts, no vendor pitches,
> unmatched networking opportunities. Visit www.blackhat.com
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] uploading more than one prediction program results

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

Hello All,

Has anyone tried uploading more than one prediction program results into 
GUS . For example I have one NAFeature_id say 45 against that I have 2 sets 
of NAlocations, one from prediction program 1 and other from prediction 
program 2. In this case If I accept the prediction program 1 result to be 
better than 2 and put it in core. algorithm for future references but  I 
still have to store the results of prediction 2 how should I do that.
Do I have to create another na_sequence_id for that particular scaffold 
which hosts that gene and upload or against the same na_sequence_id create 
another na_feature_id for the other prediction program.

Probably those worked with plasmodb can answer this.

Thanks

Sucheta

Re: [Gusdev-gusdev] Concat in gus build

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

Juan,
from what I was told you can ignore it.
Elisabetta

---

On Tue, 13 Jul 2004, Juan Perin wrote:

> When running "build GUS install -append -skipJavaCompiling" all compiles
> well, except the following warning is the last thing shown.  Is this major?
>
> Thanks
>
> [concat] Warning: Could not find any of the files specified in concat task.
>
>
>
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
> Attend Black Hat Briefings & Training, Las Vegas July 24-29 -
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>

[Gusdev-gusdev] EnzymeClass Loader Plugin

[Jonathan S. <js...@pc...>]

Jinal:

Sorry for the delay.  The plugin is  
GUS::Common::Plugin::LoadEnzymeDatabase.  We'll try to provide any  
necessary documentation, but it it meant to work with the flat file  
that you can pick up on the web.

Jonathan


------------------------------------------------------------------------ 
---
Jonathan Schug            Center for Bioinformatics
js...@pc...     Computational Biology and Informatics Lab
(215) 573-3113 voice      University of Pennsylvania,
(215) 573-3111 fax        1413 Blockley Hall, Philadelphia, PA  
19014-6021

[Gusdev-gusdev] LoadBlastSimFast.pm

[Pablo N. M. <pa...@pa...>]

Hello dev folks,
I was getting errors when running the LoadBlastSimFast plug-in. It seems
to be due to an update in the Oracle.pm.

Error msg:
Can't locate object method "nextValSql" via package
"GUS::ObjRelP::Oracle" (perhaps you forgot to load
"GUS::ObjRelP::Oracle"?) at
/var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm line
435, <GEN0> line 1654.

I found this line in the LoadBlastSimFast.pm
433:  my $nextvalSql =
$db->getDbPlatform()->nextValSql("dots.SimilaritySpan");

Then I changed to:
my $nextvalSql =
$db->getDbPlatform()->nextValVar("dots.SimilaritySpan");

Now it's working fine.

I don't know what is the standard procedure, but I'm reporting the error
so somebody with "The Power" :) who can fix and commit the changes to
the CVS.

Please let me know if there is a better way to proceed in cases like
this.

Best regards,
Pablo
-- 
-----------------------------
Pablo Nascimento Mendes
Research Scholar
Kissinger Lab
Department of Genetics
University of Georgia
C210 Life Sciences Bldg.
Athens, Georgia 30602
Phone:706 542-1447
E-mail: pa...@ug...

[Gusdev-gusdev] Concat in gus build

[Juan P. <BI...@ge...>]

When running "build GUS install -append -skipJavaCompiling" all compiles
well, except the following warning is the last thing shown.  Is this major?

Thanks

 [concat] Warning: Could not find any of the files specified in concat task.