gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] format of sequences for blast

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

Michael-

MICHAEL LUCHTAN wrote:
> and blasted the resulting retrievedSeqForBLAST file.  Now I want to load
> the results into GUS using the plugin LoadBlastSimilaritiesPK.
> This plugin requires a subject_table and a query_table.  Perhaps it is a
> question of my unfamiliarity of the whole biology aspect of what is going
> on here(I'm just a programmer), but I am not sure what these tables are
> for.  Can anybody help me
> out?

 From what I recall, the terms "query" and "subject" are taken from the wording
used in WU-BLAST output.  The query sequence is the sequence with which you are
BLASTing, and a subject sequence is one of the sequences hit/found by the BLAST
search.  Other people use different terms for these concepts (e.g., "target"
sequence instead of subject sequence) but the idea is the same.  The Similarity
table is designed to store pairwise alignments, and in the case where those
alignments are the result of a search (e.g. BLAST), you want to be able to
distinguish the query sequence from the subject/database/target sequences.  The
only added complication in GUS is that many of the references in the database
use both a table_id (to identify the table being referenced) and also a row_id
(to identify the specific row.)  The table_ids are just foreign keys into the
core.TableInfo table, which lists all of the tables in the database.

In your particular example, the query_table is DoTS.ExternalNASequence, because
that's the table from which you extracted your BLAST query sequence.  I don't
know what your subject_table will be, because I don't think you mentioned what
database you were BLASTing against.  An important thing to note is that the
plugin that loads BLAST similarities requires that all the sequences involved
be in the database already.  So if you were BLASTing against SWISS-PROT, for
example, you would first make sure that the relevant entries from SWISS-PROT
(or, to simplify matters, all of them) had been loaded into the
DoTS.ExternalAASequence table (which would then serve as your subject table.)
For a BLAST search against ProDom or CDD, you'd likely be using the MotifAASequence
table (actually a view) instead.  Let me know if this doesn't make sense,

Jonathan

Re: [Gusdev-gusdev] format of sequences for blast

[MICHAEL L. <lu...@cs...>]

Hello --

I used the following script to get some data out of GUS:
#!/usr/bin/perl

use GUS::ObjRelP::DbiDatabase;
use GUS::Common::GusConfig;

my $gusconfig=
GUS::Common::GusConfig->new("/home/luchtan/gus.properties");
my $db= GUS::ObjRelP::DbiDatabase->new($gusconfig->getDbiDsn(),

$gusconfig->getReadOnlyDatabaseLogin(),

$gusconfig->getReadOnlyDatabasePassword,
                                        1,1,1,
                                        $gusconfig->getCoreSchemaName);
my $dbh= $db->getQueryHandle();

my $idStmt= $dbh->prepare("select '>'||na_sequence_id||' '||name||'\n'
name_str,sequence from dots.externalnasequence");
$idStmt->execute();
open(TEMP, ">retrievedSeqForBLAST.tmp");
while(my (@row)=$idStmt->fetchrow_array()){
    print TEMP "@row\n";
}
close(TEMP);


and blasted the resulting retrievedSeqForBLAST file.  Now I want to load
the results into GUS using the plugin LoadBlastSimilaritiesPK.
This plugin requires a subject_table and a query_table.  Perhaps it is a
question of my unfamiliarity of the whole biology aspect of what is going
on here(I'm just a programmer), but I am not sure what these tables are
for.  Can anybody help me
out?

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Thu, 22 May 2003, Jonathan Crabtree wrote:

>
> Jessie-
>
> Jessica Kissinger wrote:
> >     If memory serves me correct, once sequences were loaded into GUS, we
> > then retrieved them along with their GUS ID to submit for blast searches.
>
> Yes, I think that's right.
>
> >     When we retrieved the sequences, we created a custom format for the
> > header line, such that the blast results once generated for these
> > sequences could be easily parsed and loaded with the existing plug-in.
> >
> >     Can someone tell me what the format of the fasta header should be,
> > i.e is it ">GUSID, External_NA _sequence Name" or the other way around
> > and should there be any formatting, tabs, spaces etc.  If I remember
> > correctly, the blast results were loaded by GUSID not "name", but I
> > don't remember.
>
> My recollection is that the defline started as you said, with ">GUSID ".
> I don't believe that the format is crucial, because (again, from what
> I remember) when you run the plugin to load the BLAST similarities you
> supply it with a regular expression that it uses to pick the GUSID
> (an na_sequence_id for most of the PlasmoDB searches) out of the defline.
> So as long as the regex matches the defline format, you should be OK,
> and I don't think that the plugin uses anything on the defline except
> for the GUSID.
>
> Jonathan
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: ObjectStore.
> If flattening out C++ or Java code to make your application fit in a
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>

Re: [Gusdev-gusdev] format of sequences for blast

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

Jessie-

Jessica Kissinger wrote:
>     If memory serves me correct, once sequences were loaded into GUS, we 
> then retrieved them along with their GUS ID to submit for blast searches.

Yes, I think that's right.

>     When we retrieved the sequences, we created a custom format for the 
> header line, such that the blast results once generated for these 
> sequences could be easily parsed and loaded with the existing plug-in.
>
>     Can someone tell me what the format of the fasta header should be, 
> i.e is it ">GUSID, External_NA _sequence Name" or the other way around 
> and should there be any formatting, tabs, spaces etc.  If I remember 
> correctly, the blast results were loaded by GUSID not "name", but I 
> don't remember.

My recollection is that the defline started as you said, with ">GUSID ".
I don't believe that the format is crucial, because (again, from what
I remember) when you run the plugin to load the BLAST similarities you
supply it with a regular expression that it uses to pick the GUSID
(an na_sequence_id for most of the PlasmoDB searches) out of the defline.
So as long as the regex matches the defline format, you should be OK,
and I don't think that the plugin uses anything on the defline except
for the GUSID.

Jonathan

[Gusdev-gusdev] format of sequences for blast

[Jessica K. <jki...@ug...>]

Hello all,

	If memory serves me correct, once sequences were loaded into 
GUS, we then retrieved them along with their GUS ID to submit for 
blast searches.

	When we retrieved the sequences, we created a custom format 
for the header line, such that the blast results once generated for 
these sequences could be easily parsed and loaded with the existing 
plug-in.

	Can someone tell me what the format of the fasta header 
should be, i.e is it ">GUSID, External_NA _sequence Name" or the 
other way around and should there be any formatting, tabs, spaces 
etc.  If I remember correctly, the blast results were loaded by GUSID 
not "name", but I don't remember.

	Thanks

	Jessie
-- 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Jessica Kissinger
Center for Tropical & Emerging Global Diseases
& Department of Genetics
University of Georgia
422 Biological Sciences
Athens, GA 30602-2606

TEL: +1 (706) 542-6562/6563
FAX: +1 (706) 542-3582
e-mail    jki...@ar...
http://www.ctegd.uga.edu/people_pages/kissinger.html
PGP-Key: http://www.arches.uga.edu/~jkissing/public_key.html
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Re: [Gusdev-gusdev] LoadPfam compile error

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

Debbie-

Deborah F. Pinney wrote:
> This isn't actually an answer to your question but an alternative plugin.  
> For the dotsbuild, we use a more generic plugin to load pfam sequences, as
> well as other sequences, into GUS,
> GUS::Common::Plugin::InsertNewExternalSequences. 
> 

I don't believe that the plugin Chetna mentioned is used to load sequences
at all; from what I remember it's just used to populate the PfamEntry table.

Jonathan

Re: [Gusdev-gusdev] LoadPfam compile error

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

Hi Chetna,

This isn't actually an answer to your question but an alternative plugin.  
For the dotsbuild, we use a more generic plugin to load pfam sequences, as
well as other sequences, into GUS,
GUS::Common::Plugin::InsertNewExternalSequences. 


Here's the bit of the pipeline that does it, you can pick out the command 
line pretty easily. It was used recently but you should always check the 
regex as they are prone to change:

 #>gnl|Pfam|pfam00291 PALP, Pyridoxal-phosphate dependent enzyme
    $regex_src_id = "^\\>\\w+\\|\\w+\\|\\w+\\s(pfam\\w+)";
    $regex_name = "^\\S+\\spfam\\w+\\,\\s([\\w\\_\\s]+)\\,\\s";
    $regex_desc = "^\\S+\\spfam\\w+\\,\\s(.*)";
    
    my $pfamArgs = "--verbose --table_name 'DoTS::MotifAASequence' 
--sequencefile '$downloadSubDir/PFAM' --external_database_release_id 
$pfamDB --regex_source_id \"$regex_src_id\" --regex_name \"$regex_name\"  
--regex_desc \"$regex_desc\"";
    
    $mgr->runPlugin("insertPfam", 
"GUS::Common::Plugin::InsertNewExternalSequences", $pfamArgs,
		   "Inserting Pfam", 'downloadGOStuff');


                                                                     
Debbie

                                                        



On Thu, 22 May 
2003,
Chetna Warade wrote:

> Hi all,
> 
> I am getting a compiler error for LoadPfam.pm
> Heres a snapshot:
> 
> [chetna@mango chetna]$ ga
> GUS::Common::Plugin::LoadPfam
> Reading properties from
> /home/gus_home/config/GUS-PluginMgr.prop
> 
> ERROR: Can't use bareword ("getArgs") as a HASH ref
> while "strict refs" in use at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> line 125.
> Compilation failed in require at (eval 1) line 1.
> 
> 
> --------------------------- STACK TRACE
> -------------------------
>        
> GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'Can\'t use bareword ("getArgs") as a HASH ref while
> "strict refs...') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 249
>        
> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 362
>        
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 284
>        
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 193
>        
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
> line 11
> [chetna@mango chetna]$
> 
> Look forward to chain of emails!,
> Chetna
> 
> 
> __________________________________
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> If flattening out C++ or Java code to make your application fit in a
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> 

[Gusdev-gusdev] LoadPfam compile error

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

Hi all,

I am getting a compiler error for LoadPfam.pm
Heres a snapshot:

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

ERROR: Can't use bareword ("getArgs") as a HASH ref
while "strict refs" in use at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
line 125.
Compilation failed in require at (eval 1) line 1.


--------------------------- STACK TRACE
-------------------------
       
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'Can\'t use bareword ("getArgs") as a HASH ref while
"strict refs...') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 249
       
GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 362
       
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 284
       
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 193
       
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
line 11
[chetna@mango chetna]$

Look forward to chain of emails!,
Chetna


__________________________________
Do you Yahoo!?
The New Yahoo! Search - Faster. Easier. Bingo.
http://search.yahoo.com

Re: [Gusdev-gusdev] Success!!

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

Excellent.  A small step for man, a giant step for pathogens.

steve

Jessica Kissinger wrote:

> Hello all,
>
>     Most of the time, in fact nearly all the time, this list is used 
> to report bugs and problems, but today, thanks to the efforts of the 
> GUS development team and the members of this list, I am pleased to 
> report success.
>
>     It has taken a while but we have successfully installed GUS 3.0, 
> loaded some data and subsequently retrieved and displayed that data 
> using the servlets.  We have come full circle.  We still have a long 
> way to go, I'm sure there are many more dependencies and command line 
> intricacies to discover, but we have made a huge first step.
>
>     Thank you
>
>     Jessie K.
> p.s. We have documented what we have learned, it will get easier.
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: ObjectStore.
> If flattening out C++ or Java code to make your application fit in a
> relational database is painful, don't do it! Check out ObjectStore.
> Now part of Progress Software. http://www.objectstore.net/sourceforge
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] Success!!

[Jessica K. <jki...@ug...>]

Hello all,

	Most of the time, in fact nearly all the time, this list is 
used to report bugs and problems, but today, thanks to the efforts of 
the GUS development team and the members of this list, I am pleased 
to report success.

	It has taken a while but we have successfully installed GUS 
3.0, loaded some data and subsequently retrieved and displayed that 
data using the servlets.  We have come full circle.  We still have a 
long way to go, I'm sure there are many more dependencies and command 
line intricacies to discover, but we have made a huge first step.

	Thank you

	Jessie K.
p.s. We have documented what we have learned, it will get easier.

[Gusdev-gusdev] adding similarity evidence to perl objects

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

Hey all, 

I was wondering if anyone knows about some of the more subtle points of 
adding evidence to GUS Objects in the Perl Object layer.  I am trying to 
add two different types of evidence to an object; one is a GUS/Perl object 
DoTS.Similarity and the other one could be one of a few random GUS/Perl 
objects.  

I notice that GUS objects have the methods addEvidence($fact) and 
addSimilarityFact($fact).  Is the latter specific to DoTS.Similarity 
objects?  Or can you choose to add those as normal Evidence?  Is there any 
particular reason that similarity gets its own evidence category?

I guess right now I am planning on adding my similarity objects as 
evidence with the addSimilarityFact() method, and the rest of my evidence 
will be added with the addEvidence() method.  Is this the right way to 
proceed given the answers to the questions above?

thanks,
Dave

Re: [Gusdev-gusdev] perl object layer:::

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

Michael-

see below.

Steve

MICHAEL LUCHTAN wrote:

>Hello all:
>A couple of q's for the FAQ:
>I'm trying to get started using the perl object layer.  I wonder if anyone
>has any documentation, like a short description of the object, followed be
>the methods that are available, and the parameters required by each
>method.  I can't seem to find this sort of documentation anywhere.  Where
>can I find this type of documentation?
>
There isn't any up-to-date documentation.  The (perl) object layer 
consists of five pieces:
  - core classes that represent a: database, database handle, database 
table database row.  These utilize the Perl DBI package.  Find these in 
$PROJECT_HOME/GUS/ObjRelP/lib/perl
  - objects that represent each GUS table and view, and rows in them. 
 Their API is pretty simple: setters and getters for attributes, get/add 
child methods; get/set parent methods.   Find these in 
$PROJECT_HOME/GUS/Model/lib/perl/*/.  
  - a superclass for all row objects.  Look here to find methods that 
are shared by all row objects.  It is: 
$PROJECT_HOME/GUS/Model/lib/perl/GusRow.pm
  - a code generator that automatically generates the GUS table and row 
objects by reading the info in the TableInfo table.  Find this in  Find 
these in $PROJECT_HOME/GUS/ObjRelP/lib/perl/generator
  - "hand-edited" objects:  these augment the automatically generated 
methods with advanced "business logic".  Find these in 
$PROJECT_HOME/GUS/Model/lib/perl/DoTS/*.pm.man

>
>Much of the code that I have seen used on the web makes use of perl
>objects from GUS2 code.  Is there a reason that
>Objects::dbiperl_utils::DbiDatabase is used instead of
>GUS::ObjRelP::DbiDatabase?
>  
>
Yes,  that was the old location of DbiDatabase in gus2 code.  It has 
been repackaged into GUS::ObjRelP::DbiDatabase to conform to the new Gus 
3 cvs structure, etc.

>Does anyone have a simple 5-10 line example code for how to login to a
>database and submit a query, printing the results?
>  
>
For basic queries, with no associated logic, we use sqlplus on the unix 
command line.  
To see how to do something like this in a script, look at 
$PROJECT_HOME/GUS/Common/bin/dumpSequencesFromTable.pl.  It issues an 
SQL query directly, not using the object layer.  To see the object layer 
in action, take a look at plugins.  

>Thanks in advance:
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: ObjectStore.
>If flattening out C++ or Java code to make your application fit in a
>relational database is painful, don't do it! Check out ObjectStore.
>Now part of Progress Software. http://www.objectstore.net/sourceforge
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] perl object layer:::

[MICHAEL L. <lu...@cs...>]

Hello all:
A couple of q's for the FAQ:
I'm trying to get started using the perl object layer.  I wonder if anyone
has any documentation, like a short description of the object, followed be
the methods that are available, and the parameters required by each
method.  I can't seem to find this sort of documentation anywhere.  Where
can I find this type of documentation?

Much of the code that I have seen used on the web makes use of perl
objects from GUS2 code.  Is there a reason that
Objects::dbiperl_utils::DbiDatabase is used instead of
GUS::ObjRelP::DbiDatabase?

Does anyone have a simple 5-10 line example code for how to login to a
database and submit a query, printing the results?


Thanks in advance:

Michael Luchtan
http://www.cs.uga.edu/~luchtan

Re: [Gusdev-gusdev] Load GOOntology error--

[MICHAEL L. <lu...@cs...>]

Hey Dave-
Seems to work!  We are commiting now.  One thing we had to do though was
to go back and comment out the ancestor hack that you mentioned before for
the new CVS checkout.  Muchos gracies for the help.

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Tue, 20 May 2003, Dave Barkan wrote:

> Hey Michael,
>
> Alright I'm pretty sure I found the problem, there was some old debugging
> code I had left in there from trying to figure out the previous problem.
> I took it out so everything should run fine.  (I think the id_file issue
> still causes a problem so this latest round wasn't a total waste of time).
>
> Just being a developer myself, and not so much dealing with how GUS is
> distributed, I'm not sure what kind of divide we're trying to keep between
> developers and users.  However, I'm sure if you encounter a problem it
> would be fine (if you are up for a challenge of going through the sometimes
> confusing plugin code) for you to try to figure it out yourself, alert
> us to it, and then we can make the change to the code.
>
> You should check out the LoadGoOntology file again from CVS and go through
> the usual steps of building/updating (outlined in a previous email).  I
> hope you have solved the update/meta problems that you encountered before?
>
> Dave
>
>
> On Tue, 20 May 2003, MICHAEL LUCHTAN wrote:
>
> > Hey Dave-
> > I haven't been running it with commit, so we don't have to worry about
> > that.  But I don't think that we've found the problem yet.  I removed the
> > --id_file that I had specified and ran the following command again:
> > [luchtan@mango luchtan]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > --id_file=/home/luchtan/GOLOG --verbose
> >
> > Unfortunately I got the same error.  Here is the output to GOLOG, followed
> > by the standard out(Please let me know if there is anything I can do to expediate the
> > sitchyation.  I'm just a little unfamiliar with the schema and kind of get
> > the feeling that ya'll want a strict divide between users and developers,
> > so I am reluctant to dive into the code):
> >
> > GOLOG:
> > Term = GO:0003673 = GO:0003673
> > Term = GO:0003674 = GO:0003674
> >
> > Stdout:
> >
> > sqlExec:
> >     UPDATE  Core.AlgorithmInvocation
> >     SET
> > 	end_time = SYSDATE,
> > 	row_alg_invocation_id = ?,
> > 	modification_date = SYSDATE
> >     WHERE   algorithm_invocation_id = ?
> >   bindValues (178, 178)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >  SQL ERROR!! involving
> >
> >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > user_write, group_write, child_term_id, row_project_id,
> > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > row_group_id )
> >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> >  Values: 6, 1, 1, 1, 2, 4, 1, 1, 178, 1, 0, 3 at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> >
> > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af100)',
> > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GORelationship ( ...')
> > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> >
> > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af100)',
> > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8d832bc)', 'ARRAY(0x8d83340)', '^J
> > INSERT INTO SRes.GORelationship (  row_user_id, other_read,...') called at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> >
> > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)',
> > 'HASH(0x8a14d7c)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > line 621
> >
> > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)')
> > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >
> > GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)')
> > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > line 271
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bfa6c)',
> > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882cd70)') called at
> > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bfa6c)',
> > 'HASH(0x882cd40)') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > 	eval {...} called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> >
> > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> >
> > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> >
> > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> >
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> > On Mon, 19 May 2003, Dave Barkan wrote:
> >
> > > Hi Michael,
> > >
> > > I figured out the problem; it's not so much the ancestor_go_term_id issue
> > > but something else instead.  It has to do with the file you specify with
> > > the --id_file flag.  This file is where GO Terms that have been loaded are
> > > written, so if you try to load more GO Terms with the same version, the
> > > plugin reads the file to skip those that have already been loaded.
> > >
> > > The problem is, if you are just testing the plugin, and not using the
> > > --commit flag (which from your provided commands, it does not appear that
> > > you are), then these processed GO ID's are still written to the file.  The
> > > quick solution is to delete the file and run the plugin again.
> > >
> > > The plugin should really get the list of processed id's from the database
> > > rather than a file; this is an optimization that we have on our to-do list
> > > but that has not been implemented.
> > >
> > > If you have been running with the --commit flag, then the solution is not
> > > so simple as just deleting the file; I actually found another bug in the
> > > process of figuring this one out.  I will fix that regardless in the next
> > > day or two, but let me know if you have been running with --commit and
> > > then I'll let you know when it's safe to re-run.
> > >
> > > If any of the above assumptions are incorrect (for example, if you have
> > > been deleting the file all along), then let me know and I'll take another
> > > look.
> > >
> > > Dave
> > >
> > >
> > > On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:
> > >
> > > > Hello-
> > > > The code needs to be changed not only on line 500, but also line 474:
> > > >     my $branchGoTerm = GUS::Model::SRes::GOTerm->new({
> > > > 	go_id  => $ancestorGoId,
> > > > 	external_database_release_id => $extDbRelId,
> > > > 	source_id => $branchRootEntry->getId(),
> > > > 	name  => $branchRootEntry->getName(), #just the name
> > > > 	definition   => $branchRootEntry->getName(),
> > > > 	minimum_level => 1,
> > > > 	maximum_level => 1,
> > > > 	number_of_levels => 1,
> > > > #	ancestor_go_term_id => $tempGusId,
> > > >
> > > > But unfortunately, this did not solve the problem.  From what I can gather
> > > > of the following log, the allowing of NULL into the ancestor_go_term_id
> > > > causes another error in GORelationship.  I imagine that this table, too,
> > > > can be modified, but wanted some feedback before going through with this.
> > > > How big a problem do you think it will cause to allow ancestor_go_term_id
> > > > in table sres.goterm to be NULL?
> > > > Here is the log:
> > > > [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > > > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > > > --id_file=/home/luchtan/GOLOG --verbose
> > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > Reading properties from /home/luchtan/gus.properties
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > >
> > > >
> > > > prepareAndExecute:     SELECT *
> > > >       FROM Core.AlgorithmImplementation
> > > >      WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
> > > >        AND cvs_revision    = '1.11.2'
> > > >
> > > >
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > >
> > > >
> > > > prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t,
> > > > Core.DatabaseInfo d where d.database_id = t.database_id
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > >
> > > > RetrieveFromDB: select * from Core.AlgorithmImplementation where
> > > > algorithm_implementation_id = ?
> > > >   bindValues (92)
> > > >
> > > >
> > > > prepareAndExecute: select login,user_id from Core.UserInfo
> > > >
> > > >
> > > > prepareAndExecute: select name,group_id from Core.GroupInfo
> > > >
> > > >
> > > > prepareAndExecute: select name,project_id from Core.ProjectInfo
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmInvocation (  end_time, row_user_id,
> > > > user_write, group_write, cpu_time, algorithm_implementation_id,
> > > > row_project_id, algorithm_invocation_id, comment_string, group_read,
> > > > row_group_id, result, other_read, cpus_used, start_time,
> > > > modification_date, user_read, row_alg_invocation_id, other_write,
> > > > machine_id )
> > > >     VALUES   (  SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, SYSDATE,
> > > > SYSDATE, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 92, 2, 176, 1, 3, pending, 1, 1, 1, 1, 0, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKey where
> > > > algorithm_implementation_id = ?
> > > >   bindValues (92)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKeyType where
> > > > algorithm_param_key_type_id = ?
> > > >   bindValues (2)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
> > > > )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1795, 345, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKeyType where
> > > > algorithm_param_key_type_id = ?
> > > >   bindValues (0)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1796, 346, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKeyType where
> > > > algorithm_param_key_type_id = ?
> > > >   bindValues (4)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, boolean_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1797, 357, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1798, 349, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1799, 353, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, boolean_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
> > > > )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1800, 347, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/gusdev/gus3.0-checkouts/GO,
> > > > 3, 1, 1, 176, 1801, 356, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1802, 360, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1803, 354, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1804, 344, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1805, 359, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/gus.properties, 3,
> > > > 1, 1, 176, 1806, 343, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/GOLOG, 3, 1, 1, 176,
> > > > 1807, 352, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, boolean_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1808, 358, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1809, 351, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1810, 348, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1811, 350, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1812, 355, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Function
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Component
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Process
> > > > Fri May 16 01:07:22 2003	loading all .ontology files in
> > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > Fri May 16 01:07:22 2003	parsing all .ontology files in preparation
> > > > for inserting into database
> > > > Fri May 16 01:07:31 2003	parsing finished; loading ontology into
> > > > database
> > > >
> > > >
> > > > prepareAndExecute: select external_database_release_id
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.690' and external_database_id = 92
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO SRes.ExternalDatabaseRelease (  row_user_id, other_read,
> > > > user_write, group_write, external_database_id, row_project_id,
> > > > modification_date, user_read, external_database_release_id,
> > > > row_alg_invocation_id, group_read, version, other_write, row_group_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 1, 92, 2, 1, 95, 176, 1, 2.690, 0, 3)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > Fri May 16 01:07:31 2003	successfully submitted new entry into
> > > > SRes.ExternalDatabaseReleaseId with primary key of 95
> > > >
> > > > Fri May 16 01:07:31 2003	making root node for function
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write,
> > > > group_write, row_project_id, name, external_database_release_id,
> > > > 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, other_write, definition )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?,
> > > > ?, ?, ? )
> > > >   bindValues (6, GO:0003674, 1, 1, 2, molecular_function, 95, 1, 1, 3, 6,
> > > > 1, GO:0003674, 1, 176, 1, 1, 0, molecular_function)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > prepareAndExecute: Update SRes.GOTerm Set ancestor_go_term_id = 6
> > > >                where external_database_release_id = 95
> > > >                and go_term_id = 6
> > > > Fri May 16 01:07:31 2003	loading GO Terms into SRes.GOTerm
> > > >
> > > >
> > > > prepareAndExecute: select go_relationship_type_id, name
> > > >                from sres.gorelationshiptype
> > > > Fri May 16 01:07:31 2003	loading hierarchy and synonyms into
> > > > SRes.GORelationship and SRes.GOSynonym
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > > > user_write, group_write, child_term_id, row_project_id,
> > > > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > > > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > > > row_group_id )
> > > >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> > > >   bindValues (6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3)
> > > > DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> > > > ("SRES"."GORELATIONSHIP"."PARENT_TERM_ID") (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
> > > >
> > > >
> > > > sqlExec:
> > > >     UPDATE  Core.AlgorithmInvocation
> > > >     SET
> > > > 	end_time = SYSDATE,
> > > > 	row_alg_invocation_id = ?,
> > > > 	modification_date = SYSDATE
> > > >     WHERE   algorithm_invocation_id = ?
> > > >   bindValues (176, 176)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >  SQL ERROR!! involving
> > > >
> > > >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > > > user_write, group_write, child_term_id, row_project_id,
> > > > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > > > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > > > row_group_id )
> > > >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> > > >  Values: 6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3 at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> > > >
> > > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
> > > > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GORelationship ( ...')
> > > > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> > > >
> > > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
> > > > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8b73214)', 'ARRAY(0x8b73298)', '^J
> > > > INSERT INTO SRes.GORelationship (  row_user_id, other_read,...') called at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> > > >
> > > > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)',
> > > > 'HASH(0x896950c)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > > > line 621
> > > >
> > > > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
> > > > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> > > >
> > > > GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
> > > > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > > > line 271
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ceb4)') called at
> > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'HASH(0x882ce84)') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > > > 	eval {...} called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> > > >
> > > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> > > >
> > > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> > > >
> > > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> > > >
> > > >
> > > > Thanks,
> > > >
> > > > Michael Luchtan
> > > > http://www.cs.uga.edu/~luchtan
> > > >
> > > >
> > > > On Fri, 16 May 2003, Dave Barkan wrote:
> > > >
> > > > > Hi Michael and folks,
> > > > >
> > > > > This is the result of a known bug in the database schema.  Right now,
> > > > > there is a non-nullable foreign key in SRes.GoTerm that points back to
> > > > > SRes.GoTerm itself (the foreign key being ancestor_go_term).
> > > > >
> > > > > I believe I submitted a request for a schema change, but until that change
> > > > > is implemented the temporary solution is a hack; when loading the root
> > > > > term of the GO Ontology, I just set the ancestor_go_term to 1, so that it
> > > > > temporarily points to whatever entry is in SRes.GoTerm with an ID of 1.
> > > > > Then I immediately update the root entry to (correctly) point to itself as
> > > > > the ancestor_go_term.
> > > > >
> > > > > However, since you are loading the Ontology for the first time, you
> > > > > obviously won't have any entry with an ID of 1; that is the cause of the
> > > > > error message you are getting.
> > > > >
> > > > > I think the only solution to this is to make the column ancestor_go_term
> > > > > nullable.  After that, you will have to take out the line in the plugin
> > > > > that does that does the hack of setting the ancestor_go_term to 1, which
> > > > > is shown here:
> > > > >
> > > > > (line 500 of LoadGoOntology.pm):
> > > > >
> > > > >  my $ontologyGoTerm = GUS::Model::SRes::GOTerm->new({
> > > > > 	go_id  => $rootGoId,
> > > > > 	external_database_release_id => $extDbRelId,
> > > > > 	source_id => $rootEntry->getId(),
> > > > > 	name  => $rootEntry->getName(), #just the name
> > > > > 	definition   => $rootEntry->getName(),
> > > > > 	minimum_level => 0,
> > > > > 	maximum_level => 0,
> > > > > 	number_of_levels => 1,
> > > > > 	ancestor_go_term_id => $tempAncestorId,  #remove this line
> > > > >     } );
> > > > >
> > > > > After reading some of the previous email traffic on the gus-dev list, I'm
> > > > > not sure if you have permissions to make these modifications.  I can make
> > > > > them for you and resubmit them to cvs, but I am hesitant to make this
> > > > > change permanent until we have the schema change to make the column
> > > > > non-nullable instituted in our copy of GUS.  This brings up some of the
> > > > > larger questions about how schema changes to GUS are ensured to remain
> > > > > consistent among all copies of GUS. I'm sure there's a protocol; while I'm
> > > > > not familiar with it I'm sure other people on this list are and could
> > > > > help you out implementing all of this.
> > > > >
> > > > > Glad you got the plugin running; did you end up passing in the external
> > > > > database ids as command line parameters or did you figure out what was
> > > > > causing the previous problem some other way?
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > >
> > > > > On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:
> > > > >
> > > > > > Dave-
> > > > > > Check it out:
> > > > > > [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > > > > > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > > > > > --id_file=/home/luchtan/GOLOG --verbose
> > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > >
> > > > >
> > > > > > executing Select external_database_id from sres.externaldatabase where
> > > > > > name = ? GO Function
> > > > > > executing Select external_database_id from sres.externaldatabase where
> > > > > > name = ? GO Component
> > > > > > executing Select external_database_id from sres.externaldatabase where
> > > > > > name = ? GO Process
> > > > > > Thu May 15 23:59:40 2003	loading all .ontology files in
> > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > Thu May 15 23:59:40 2003	parsing all .ontology files in preparation
> > > > > > for inserting into database
> > > > > > Thu May 15 23:59:49 2003	parsing finished; loading ontology into
> > > > > > database
> > > > > >
> > > > > >
> > > > > > prepareAndExecute: select external_database_release_id
> > > > > >                from sres.externalDatabaseRelease
> > > > > >                where version = '2.690' and external_database_id = 92
> > > > > >
> > > > >
> > > > > > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology)
> > > > > > DBD::Oracle::st execute failed: ORA-02291: integrity constraint
> > > > > > (SRES.GOTERM_FK02) violated - parent key not found (DBD ERROR:
> > > > > > OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
> > > > > > 144.
> > > > > >
> > > > > >
> > > > > > sqlExec:
> > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > >     SET
> > > > > > 	end_time = SYSDATE,
> > > > > > 	row_alg_invocation_id = ?,
> > > > > > 	modification_date = SYSDATE
> > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > >   bindValues (174, 174)
> > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > >
> > > > > >  SQL ERROR!! involving
> > > > > >
> > > > > >     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, 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, other_write,
> > > > > > definition )
> > > > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
> > > > > > ?, ?, ?, ? )
> > > > > >  Values: 6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
> > > > > > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> > > > > >
> > > > > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > > > > > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GOTerm (  row_use...')
> > > > > > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> > > > > >
> > > > > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > > > > > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8bc753c)', 'ARRAY(0x8bc75c0)', '^J
> > > > > > INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, ...') called at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> > > > > >
> > > > > > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)',
> > > > > > 'HASH(0x890dc40)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > > > > > line 621
> > > > > >
> > > > > > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > > > > > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> > > > > >
> > > > > > GUS::Model::GusRow::submit('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > > > > > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > > > > > line 512
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::__makeOntologyRoot('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'HASH(0x8e7c514)', 'GO:0003673', 93) called at
> > > > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 437
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::__makeRoots('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'HASH(0x8e7c514)', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x8b26f04)',
> > > > > > 93, undef, 'FileHandle=GLOB(0x88c801c)') called at
> > > > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 195
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ce64)') called at
> > > > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'HASH(0x882ce34)') called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > > > > > 	eval {...} called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> > > > > >
> > > > > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> > > > > >
> > > > > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> > > > > >
> > > > > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > > > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> > > > > >
> > > > > >
> > > > > > Looks like an sql error, but I'm not sure what to do about it.  Do any of
> > > > > > the rror messages give you any leads?
> > > > > >
> > > > > >
> > > > > > Michael Luchtan
> > > > > > http://www.cs.uga.edu/~luchtan
> > > > > >
> > > > > >
> > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > >
> > > > > > > Hey Michael,
> > > > > > >
> > > > > > > I still think that the error is an sql error.  It does say
> > > > > > >
> > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > >
> > > > > > > but my experience is that that message is printed out when the sql
> > > > > > > statement is not what it expects.  The fact that it also says
> > > > > > >
> > > > > > >  prepareAndExecute: select external_database_release_id
> > > > > > > >                from sres.externalDatabaseRelease
> > > > > > > >                where version = '2.690' and external_database_id =
> > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > >
> > > > > > > and doesn't print out the external_database_id in the statement is why I
> > > > > > > am focusing on the external database issue.  Here's what I did so we can
> > > > > > > narrow it down:
> > > > > > >
> > > > > > > 1.  I added an error statement if the plugin tries to run this query and
> > > > > > > can't find the database id; that way we can be sure about the problem.
> > > > > > >
> > > > > > > 2.  I added three command line arguments: function_db_id, process_db_id,
> > > > > > > and component_db_id.  You can pass these in to specify the external
> > > > > > > database ids of the respective branches, thus avoiding the
> > > > > > > programming hack of hardcoded entries in the database.
> > > > > > >
> > > > > > > To rerun, just do the following:
> > > > > > >
> > > > > > > 1. cvs update LoadGoOntology to get the version I just committed.
> > > > > > > 2. run 'build GUS/GOPredict install -append' to build the plugin.
> > > > > > > 3. run the command 'ga +update GUS::GOPredict::Plugin::LoadGoOntology
> > > > > > > --commit'
> > > > > > >
> > > > > > > (this sequence of commands generally has to be done whenever changes have
> > > > > > > been made to a plugin, especially those to the command line arguments).
> > > > > > >
> > > > > > > Try that, run it with the --verbose flag set, and let me know what you
> > > > > > > see.
> > > > > > >
> > > > > > > Dave
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > > > >
> > > > > > > > Dave-
> > > > > > > >
> > > > > > > > Yes, we ran the provided queries, and they are in the table.  Also, those
> > > > > > > > files are there as downloaded from the ftp site that you provided.
> > > > > > > > Again, here is a snapshot of where it failed(which seems more like a
> > > > > > > > compiler error than an sql error):
> > > > > > > >
> > > > > > > > sqlExec:
> > > > > > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > > > > > group_write, is_default, order_num, row_project_id,
> > > > > > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > > > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > > > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > > > > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > > > > > >   bindValues (6, 1, 1, 0, 0, 2, 169, 1, 3, 1, 1, 169, 1740, 304, 0)
> > > > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > > > Thu May 15 03:01:35 2003	loading all .ontology files in
> > > > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > > > Thu May 15 03:01:35 2003	parsing all .ontology files in preparation
> > > > > > > > for inserting into database
> > > > > > > > Thu May 15 03:01:43 2003	parsing finished; loading ontology into
> > > > > > > > database
> > > > > > > >
> > > > > > > >
> > > > > > > > prepareAndExecute: select external_database_release_id
> > > > > > > >                from sres.externalDatabaseRelease
> > > > > > > >                where version = '2.690' and external_database_id =
> > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > prepareAndExecute FAILED:
> > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2074)->errstr
> > > > > > > >
> > > > > > > >
> > > > > > > > sqlExec:
> > > > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > > > >     SET
> > > > > > > > 	end_time = SYSDATE,
> > > > > > > > 	row_alg_invocation_id = ?,
> > > > > > > > 	modification_date = SYSDATE
> > > > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > > > >   bindValues (169, 169)
> > > > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > >
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > >
> > > > > > > > Michael Luchtan
> > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > >
> > > > > > > >
> > > > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > > > >
> > > > > > > > > Hey Michael,
> > > > > > > > >
> > > > > > > > > Alright, I'm still not sure it isn't an issue with an external database
> > > > > > > > > entry.  Try these two things.
> > > > > > > > >
> > > > > > > > > 1.Run the query 'select external_database_id from sres.externaldatabase
> > > > > > > > > where name = ?'
> > > > > > > > >
> > > > > > > > > and substitute 'GO Function,' GO Process,' 'GO Component' for each ?.
> > > > > > > > >
> > > > > > > > > 2. Make sure that the ontology files you are loading from are of the form
> > > > > > > > > 'branch.ontology' where branch can be one of 'process', 'function', or
> > > > > > > > > 'component.' These are the names of the files when they are downloaded
> > > > > > > > > from the GO site.
> > > > > > > > >
> > > > > > > > > The reason I want you to give the query a shot is that the plugin runs the
> > > > > > > > > same query to get the id's of those databases.  Then it turns around and
> > > > > > > > > uses those ids in the query that is failing:
> > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > prepareAndExecute: select external_database_release_id
> > > > > > > > > >                from sres.externalDatabaseRelease
> > > > > > > > > >                where version = '2.690' and external_database_id =
> > > > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > >
> > > > > > > > > Sorry if this is overkill to try to figure this one out but I guess that's
> > > > > > > > > the disadvantage of debugging across state lines!
> > > > > > > > >
> > > > > > > > > dave
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > > > prepareAndExecute FAILED:
> > > > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2084)->errstr
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > sqlExec:
> > > > > > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > > > > > >     SET
> > > > > > > > > > 	end_time = SYSDATE,
> > > > > > > > > > 	row_alg_invocation_id = ?,
> > > > > > > > > > 	modification_date = SYSDATE
> > > > > > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > > > > > >   bindValues (167, 167)
> > > > > > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Michael Luchtan
> > > > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > > > > > >
> > > > > > > > > > > Hey Michael,
> > > > > > > > > > >
> > > > > > > > > > > Can you run it again with the --verbose flag set, and resend the output?
> > > > > > > > > > > That will probably help me figure out the error much easier.  Thanks,
> > > > > > > > > > >
> > > > > > > > > > > Dave
> > > > > > > > > > >
> > > > > > > > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > > > > > > > >
> > > > > > > > > > > > Hello Dave-
> > > > > > > > > > > > Here is the error:
> > > > > > > > > > > >
> > > > > > > > > > > > [luchtan@mango gbparserFailures]$ ga
> > > > > > > > > > > > GUS::GOPredict::Plugin::LoadGoOntology --create_release
> > > > > > > > > > > > --file_path=/home/gusdev/gus3.0-checkouts/GO --id_file=/home/luchtan/GOLOG
> > > > > > > > > > > >
> > > > > > > > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > > > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > Thu May 15 00:48:36 2003	loading all .ontology files in
> > > > > > > > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > > > > > > > Thu May 15 00:48:36 2003	parsing all .ontology files in preparation
> > > > > > > > > > > > for inserting into database
> > > > > > > > > > > > Thu May 15 00:48:44 2003	parsing finished; loading ontology into
> > > > > > > > > > > > database
> > > > > > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > > > > > prepareAndExecute FAILED:
> > > > > > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2150)->errstr
> > > > > > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > > > > > >
> > > > > > > > > > > > Some kind of referencing error?  Thanks,
> > > > > > > > > > > >
> > > > > > > > > > > > Michael Luchtan
> > > > > > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > -------------------------------------------------------
> > > > > > > > > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > > > > > > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > > > > > > > > www.enterpriselinuxforum.com
> > > > > > > > > > > >
> > > > > > > > > > > > _______________________________________________
> > > > > > > > > > > > Gusdev-gusdev mailing list
> > > > > > > > > > > > Gus...@li...
> > > > > > > > > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > -------------------------------------------------------
> > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > www.enterpriselinuxforum.com
> > > > >
> > > > > _______________________________________________
> > > > > Gusdev-gusdev mailing list
> > > > > Gus...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > >
> > > >
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > www.enterpriselinuxforum.com
> > > >
> > > > _______________________________________________
> > > > Gusdev-gusdev mailing list
> > > > Gus...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > >
> > >
> > >
> >
> >
> >
> > -------------------------------------------------------
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> > relational database is painful, don't do it! Check out ObjectStore.
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> >
>
>

Re: [Gusdev-gusdev] Load GOOntology error--

[MICHAEL L. <lu...@cs...>]

Hey Dave-
I haven't been running it with commit, so we don't have to worry about
that.  But I don't think that we've found the problem yet.  I removed the
--id_file that I had specified and ran the following command again:
[luchtan@mango luchtan]$ ga GUS::GOPredict::Plugin::LoadGoOntology
--create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
--id_file=/home/luchtan/GOLOG --verbose

Unfortunately I got the same error.  Here is the output to GOLOG, followed
by the standard out(Please let me know if there is anything I can do to expediate the
sitchyation.  I'm just a little unfamiliar with the schema and kind of get
the feeling that ya'll want a strict divide between users and developers,
so I am reluctant to dive into the code):

GOLOG:
Term = GO:0003673 = GO:0003673
Term = GO:0003674 = GO:0003674

Stdout:

sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (178, 178)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

 SQL ERROR!! involving

    INSERT INTO SRes.GORelationship (  row_user_id, other_read,
user_write, group_write, child_term_id, row_project_id,
go_relationship_id, modification_date, go_relationship_type_id, user_read,
row_alg_invocation_id, group_read, parent_term_id, other_write,
row_group_id )
    VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
 Values: 6, 1, 1, 1, 2, 4, 1, 1, 178, 1, 0, 3 at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af100)',
'^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GORelationship ( ...')
called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af100)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8d832bc)', 'ARRAY(0x8d83340)', '^J
INSERT INTO SRes.GORelationship (  row_user_id, other_read,...') called at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)',
'HASH(0x8a14d7c)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 621

GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677

GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)')
called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
line 271

GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bfa6c)',
'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882cd70)') called at
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144

GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bfa6c)',
'HASH(0x882cd40)') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
	eval {...} called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::GOPredict::Plugin::LoadGoOntology') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::GOPredict::Plugin::LoadGoOntology') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11


Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Mon, 19 May 2003, Dave Barkan wrote:

> Hi Michael,
>
> I figured out the problem; it's not so much the ancestor_go_term_id issue
> but something else instead.  It has to do with the file you specify with
> the --id_file flag.  This file is where GO Terms that have been loaded are
> written, so if you try to load more GO Terms with the same version, the
> plugin reads the file to skip those that have already been loaded.
>
> The problem is, if you are just testing the plugin, and not using the
> --commit flag (which from your provided commands, it does not appear that
> you are), then these processed GO ID's are still written to the file.  The
> quick solution is to delete the file and run the plugin again.
>
> The plugin should really get the list of processed id's from the database
> rather than a file; this is an optimization that we have on our to-do list
> but that has not been implemented.
>
> If you have been running with the --commit flag, then the solution is not
> so simple as just deleting the file; I actually found another bug in the
> process of figuring this one out.  I will fix that regardless in the next
> day or two, but let me know if you have been running with --commit and
> then I'll let you know when it's safe to re-run.
>
> If any of the above assumptions are incorrect (for example, if you have
> been deleting the file all along), then let me know and I'll take another
> look.
>
> Dave
>
>
> On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:
>
> > Hello-
> > The code needs to be changed not only on line 500, but also line 474:
> >     my $branchGoTerm = GUS::Model::SRes::GOTerm->new({
> > 	go_id  => $ancestorGoId,
> > 	external_database_release_id => $extDbRelId,
> > 	source_id => $branchRootEntry->getId(),
> > 	name  => $branchRootEntry->getName(), #just the name
> > 	definition   => $branchRootEntry->getName(),
> > 	minimum_level => 1,
> > 	maximum_level => 1,
> > 	number_of_levels => 1,
> > #	ancestor_go_term_id => $tempGusId,
> >
> > But unfortunately, this did not solve the problem.  From what I can gather
> > of the following log, the allowing of NULL into the ancestor_go_term_id
> > causes another error in GORelationship.  I imagine that this table, too,
> > can be modified, but wanted some feedback before going through with this.
> > How big a problem do you think it will cause to allow ancestor_go_term_id
> > in table sres.goterm to be NULL?
> > Here is the log:
> > [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > --id_file=/home/luchtan/GOLOG --verbose
> > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > Reading properties from /home/luchtan/gus.properties
> > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> >
> >
> > prepareAndExecute:     SELECT *
> >       FROM Core.AlgorithmImplementation
> >      WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
> >        AND cvs_revision    = '1.11.2'
> >
> >
> > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> >
> >
> > prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t,
> > Core.DatabaseInfo d where d.database_id = t.database_id
> > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> >
> > RetrieveFromDB: select * from Core.AlgorithmImplementation where
> > algorithm_implementation_id = ?
> >   bindValues (92)
> >
> >
> > prepareAndExecute: select login,user_id from Core.UserInfo
> >
> >
> > prepareAndExecute: select name,group_id from Core.GroupInfo
> >
> >
> > prepareAndExecute: select name,project_id from Core.ProjectInfo
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmInvocation (  end_time, row_user_id,
> > user_write, group_write, cpu_time, algorithm_implementation_id,
> > row_project_id, algorithm_invocation_id, comment_string, group_read,
> > row_group_id, result, other_read, cpus_used, start_time,
> > modification_date, user_read, row_alg_invocation_id, other_write,
> > machine_id )
> >     VALUES   (  SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, SYSDATE,
> > SYSDATE, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 92, 2, 176, 1, 3, pending, 1, 1, 1, 1, 0, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> > getRelations: select * from Core.AlgorithmParamKey where
> > algorithm_implementation_id = ?
> >   bindValues (92)
> >
> > getRelations: select * from Core.AlgorithmParamKeyType where
> > algorithm_param_key_type_id = ?
> >   bindValues (2)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, int_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
> > )
> >   bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1795, 345, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> > getRelations: select * from Core.AlgorithmParamKeyType where
> > algorithm_param_key_type_id = ?
> >   bindValues (0)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1796, 346, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> > getRelations: select * from Core.AlgorithmParamKeyType where
> > algorithm_param_key_type_id = ?
> >   bindValues (4)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, boolean_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1797, 357, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, int_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1798, 349, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, int_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1799, 353, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, boolean_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
> > )
> >   bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1800, 347, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/gusdev/gus3.0-checkouts/GO,
> > 3, 1, 1, 176, 1801, 356, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1802, 360, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, int_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1803, 354, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, int_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1804, 344, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1805, 359, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/gus.properties, 3,
> > 1, 1, 176, 1806, 343, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/GOLOG, 3, 1, 1, 176,
> > 1807, 352, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, boolean_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1808, 358, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, int_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1809, 351, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id, int_value,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1810, 348, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1811, 350, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1812, 355, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > executing Select external_database_id from sres.externaldatabase where
> > name = ? GO Function
> > executing Select external_database_id from sres.externaldatabase where
> > name = ? GO Component
> > executing Select external_database_id from sres.externaldatabase where
> > name = ? GO Process
> > Fri May 16 01:07:22 2003	loading all .ontology files in
> > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > Fri May 16 01:07:22 2003	parsing all .ontology files in preparation
> > for inserting into database
> > Fri May 16 01:07:31 2003	parsing finished; loading ontology into
> > database
> >
> >
> > prepareAndExecute: select external_database_release_id
> >                from sres.externalDatabaseRelease
> >                where version = '2.690' and external_database_id = 92
> >
> >
> > sqlExec:
> >     INSERT INTO SRes.ExternalDatabaseRelease (  row_user_id, other_read,
> > user_write, group_write, external_database_id, row_project_id,
> > modification_date, user_read, external_database_release_id,
> > row_alg_invocation_id, group_read, version, other_write, row_group_id )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 1, 92, 2, 1, 95, 176, 1, 2.690, 0, 3)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > Fri May 16 01:07:31 2003	successfully submitted new entry into
> > SRes.ExternalDatabaseReleaseId with primary key of 95
> >
> > Fri May 16 01:07:31 2003	making root node for function
> >
> >
> > sqlExec:
> >     INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write,
> > group_write, row_project_id, name, external_database_release_id,
> > 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, other_write, definition )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?,
> > ?, ?, ? )
> >   bindValues (6, GO:0003674, 1, 1, 2, molecular_function, 95, 1, 1, 3, 6,
> > 1, GO:0003674, 1, 176, 1, 1, 0, molecular_function)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >
> > prepareAndExecute: Update SRes.GOTerm Set ancestor_go_term_id = 6
> >                where external_database_release_id = 95
> >                and go_term_id = 6
> > Fri May 16 01:07:31 2003	loading GO Terms into SRes.GOTerm
> >
> >
> > prepareAndExecute: select go_relationship_type_id, name
> >                from sres.gorelationshiptype
> > Fri May 16 01:07:31 2003	loading hierarchy and synonyms into
> > SRes.GORelationship and SRes.GOSynonym
> >
> >
> > sqlExec:
> >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > user_write, group_write, child_term_id, row_project_id,
> > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > row_group_id )
> >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> >   bindValues (6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3)
> > DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> > ("SRES"."GORELATIONSHIP"."PARENT_TERM_ID") (DBD ERROR: OCIStmtExecute) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
> >
> >
> > sqlExec:
> >     UPDATE  Core.AlgorithmInvocation
> >     SET
> > 	end_time = SYSDATE,
> > 	row_alg_invocation_id = ?,
> > 	modification_date = SYSDATE
> >     WHERE   algorithm_invocation_id = ?
> >   bindValues (176, 176)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >  SQL ERROR!! involving
> >
> >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > user_write, group_write, child_term_id, row_project_id,
> > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > row_group_id )
> >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> >  Values: 6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3 at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> >
> > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
> > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GORelationship ( ...')
> > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> >
> > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
> > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8b73214)', 'ARRAY(0x8b73298)', '^J
> > INSERT INTO SRes.GORelationship (  row_user_id, other_read,...') called at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> >
> > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)',
> > 'HASH(0x896950c)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > line 621
> >
> > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
> > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >
> > GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
> > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > line 271
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ceb4)') called at
> > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > 'HASH(0x882ce84)') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > 	eval {...} called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> >
> > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> >
> > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> >
> > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> >
> >
> > Thanks,
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> > On Fri, 16 May 2003, Dave Barkan wrote:
> >
> > > Hi Michael and folks,
> > >
> > > This is the result of a known bug in the database schema.  Right now,
> > > there is a non-nullable foreign key in SRes.GoTerm that points back to
> > > SRes.GoTerm itself (the foreign key being ancestor_go_term).
> > >
> > > I believe I submitted a request for a schema change, but until that change
> > > is implemented the temporary solution is a hack; when loading the root
> > > term of the GO Ontology, I just set the ancestor_go_term to 1, so that it
> > > temporarily points to whatever entry is in SRes.GoTerm with an ID of 1.
> > > Then I immediately update the root entry to (correctly) point to itself as
> > > the ancestor_go_term.
> > >
> > > However, since you are loading the Ontology for the first time, you
> > > obviously won't have any entry with an ID of 1; that is the cause of the
> > > error message you are getting.
> > >
> > > I think the only solution to this is to make the column ancestor_go_term
> > > nullable.  After that, you will have to take out the line in the plugin
> > > that does that does the hack of setting the ancestor_go_term to 1, which
> > > is shown here:
> > >
> > > (line 500 of LoadGoOntology.pm):
> > >
> > >  my $ontologyGoTerm = GUS::Model::SRes::GOTerm->new({
> > > 	go_id  => $rootGoId,
> > > 	external_database_release_id => $extDbRelId,
> > > 	source_id => $rootEntry->getId(),
> > > 	name  => $rootEntry->getName(), #just the name
> > > 	definition   => $rootEntry->getName(),
> > > 	minimum_level => 0,
> > > 	maximum_level => 0,
> > > 	number_of_levels => 1,
> > > 	ancestor_go_term_id => $tempAncestorId,  #remove this line
> > >     } );
> > >
> > > After reading some of the previous email traffic on the gus-dev list, I'm
> > > not sure if you have permissions to make these modifications.  I can make
> > > them for you and resubmit them to cvs, but I am hesitant to make this
> > > change permanent until we have the schema change to make the column
> > > non-nullable instituted in our copy of GUS.  This brings up some of the
> > > larger questions about how schema changes to GUS are ensured to remain
> > > consistent among all copies of GUS. I'm sure there's a protocol; while I'm
> > > not familiar with it I'm sure other people on this list are and could
> > > help you out implementing all of this.
> > >
> > > Glad you got the plugin running; did you end up passing in the external
> > > database ids as command line parameters or did you figure out what was
> > > causing the previous problem some other way?
> > >
> > > Dave
> > >
> > >
> > >
> > > On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:
> > >
> > > > Dave-
> > > > Check it out:
> > > > [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > > > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > > > --id_file=/home/luchtan/GOLOG --verbose
> > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > Reading properties from /home/luchtan/gus.properties
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > >
> > >
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Function
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Component
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Process
> > > > Thu May 15 23:59:40 2003	loading all .ontology files in
> > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > Thu May 15 23:59:40 2003	parsing all .ontology files in preparation
> > > > for inserting into database
> > > > Thu May 15 23:59:49 2003	parsing finished; loading ontology into
> > > > database
> > > >
> > > >
> > > > prepareAndExecute: select external_database_release_id
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.690' and external_database_id = 92
> > > >
> > >
> > > > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology)
> > > > DBD::Oracle::st execute failed: ORA-02291: integrity constraint
> > > > (SRES.GOTERM_FK02) violated - parent key not found (DBD ERROR:
> > > > OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
> > > > 144.
> > > >
> > > >
> > > > sqlExec:
> > > >     UPDATE  Core.AlgorithmInvocation
> > > >     SET
> > > > 	end_time = SYSDATE,
> > > > 	row_alg_invocation_id = ?,
> > > > 	modification_date = SYSDATE
> > > >     WHERE   algorithm_invocation_id = ?
> > > >   bindValues (174, 174)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >  SQL ERROR!! involving
> > > >
> > > >     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, 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, other_write,
> > > > definition )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
> > > > ?, ?, ?, ? )
> > > >  Values: 6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
> > > > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> > > >
> > > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > > > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GOTerm (  row_use...')
> > > > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> > > >
> > > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > > > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8bc753c)', 'ARRAY(0x8bc75c0)', '^J
> > > > INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, ...') called at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> > > >
> > > > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)',
> > > > 'HASH(0x890dc40)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > > > line 621
> > > >
> > > > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > > > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> > > >
> > > > GUS::Model::GusRow::submit('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > > > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > > > line 512
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::__makeOntologyRoot('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'HASH(0x8e7c514)', 'GO:0003673', 93) called at
> > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 437
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::__makeRoots('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'HASH(0x8e7c514)', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x8b26f04)',
> > > > 93, undef, 'FileHandle=GLOB(0x88c801c)') called at
> > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 195
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ce64)') called at
> > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'HASH(0x882ce34)') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > > > 	eval {...} called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> > > >
> > > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> > > >
> > > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> > > >
> > > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> > > >
> > > >
> > > > Looks like an sql error, but I'm not sure what to do about it.  Do any of
> > > > the rror messages give you any leads?
> > > >
> > > >
> > > > Michael Luchtan
> > > > http://www.cs.uga.edu/~luchtan
> > > >
> > > >
> > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > >
> > > > > Hey Michael,
> > > > >
> > > > > I still think that the error is an sql error.  It does say
> > > > >
> > > > > > Can't call method "execute" without a package or object reference at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > >
> > > > > but my experience is that that message is printed out when the sql
> > > > > statement is not what it expects.  The fact that it also says
> > > > >
> > > > >  prepareAndExecute: select external_database_release_id
> > > > > >                from sres.externalDatabaseRelease
> > > > > >                where version = '2.690' and external_database_id =
> > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > >
> > > > > and doesn't print out the external_database_id in the statement is why I
> > > > > am focusing on the external database issue.  Here's what I did so we can
> > > > > narrow it down:
> > > > >
> > > > > 1.  I added an error statement if the plugin tries to run this query and
> > > > > can't find the database id; that way we can be sure about the problem.
> > > > >
> > > > > 2.  I added three command line arguments: function_db_id, process_db_id,
> > > > > and component_db_id.  You can pass these in to specify the external
> > > > > database ids of the respective branches, thus avoiding the
> > > > > programming hack of hardcoded entries in the database.
> > > > >
> > > > > To rerun, just do the following:
> > > > >
> > > > > 1. cvs update LoadGoOntology to get the version I just committed.
> > > > > 2. run 'build GUS/GOPredict install -append' to build the plugin.
> > > > > 3. run the command 'ga +update GUS::GOPredict::Plugin::LoadGoOntology
> > > > > --commit'
> > > > >
> > > > > (this sequence of commands generally has to be done whenever changes have
> > > > > been made to a plugin, especially those to the command line arguments).
> > > > >
> > > > > Try that, run it with the --verbose flag set, and let me know what you
> > > > > see.
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > >
> > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > >
> > > > > > Dave-
> > > > > >
> > > > > > Yes, we ran the provided queries, and they are in the table.  Also, those
> > > > > > files are there as downloaded from the ftp site that you provided.
> > > > > > Again, here is a snapshot of where it failed(which seems more like a
> > > > > > compiler error than an sql error):
> > > > > >
> > > > > > sqlExec:
> > > > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > > > group_write, is_default, order_num, row_project_id,
> > > > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > > > >   bindValues (6, 1, 1, 0, 0, 2, 169, 1, 3, 1, 1, 169, 1740, 304, 0)
> > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > Thu May 15 03:01:35 2003	loading all .ontology files in
> > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > Thu May 15 03:01:35 2003	parsing all .ontology files in preparation
> > > > > > for inserting into database
> > > > > > Thu May 15 03:01:43 2003	parsing finished; loading ontology into
> > > > > > database
> > > > > >
> > > > > >
> > > > > > prepareAndExecute: select external_database_release_id
> > > > > >                from sres.externalDatabaseRelease
> > > > > >                where version = '2.690' and external_database_id =
> > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > prepareAndExecute FAILED:
> > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2074)->errstr
> > > > > >
> > > > > >
> > > > > > sqlExec:
> > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > >     SET
> > > > > > 	end_time = SYSDATE,
> > > > > > 	row_alg_invocation_id = ?,
> > > > > > 	modification_date = SYSDATE
> > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > >   bindValues (169, 169)
> > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > Can't call method "execute" without a package or object reference at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > >
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Michael Luchtan
> > > > > > http://www.cs.uga.edu/~luchtan
> > > > > >
> > > > > >
> > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > >
> > > > > > > Hey Michael,
> > > > > > >
> > > > > > > Alright, I'm still not sure it isn't an issue with an external database
> > > > > > > entry.  Try these two things.
> > > > > > >
> > > > > > > 1.Run the query 'select external_database_id from sres.externaldatabase
> > > > > > > where name = ?'
> > > > > > >
> > > > > > > and substitute 'GO Function,' GO Process,' 'GO Component' for each ?.
> > > > > > >
> > > > > > > 2. Make sure that the ontology files you are loading from are of the form
> > > > > > > 'branch.ontology' where branch can be one of 'process', 'function', or
> > > > > > > 'component.' These are the names of the files when they are downloaded
> > > > > > > from the GO site.
> > > > > > >
> > > > > > > The reason I want you to give the query a shot is that the plugin runs the
> > > > > > > same query to get the id's of those databases.  Then it turns around and
> > > > > > > uses those ids in the query that is failing:
> > > > > > >
> > > > > > > >
> > > > > > > > prepareAndExecute: select external_database_release_id
> > > > > > > >                from sres.externalDatabaseRelease
> > > > > > > >                where version = '2.690' and external_database_id =
> > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > >
> > > > > > > Sorry if this is overkill to try to figure this one out but I guess that's
> > > > > > > the disadvantage of debugging across state lines!
> > > > > > >
> > > > > > > dave
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > prepareAndExecute FAILED:
> > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2084)->errstr
> > > > > > > >
> > > > > > > >
> > > > > > > > sqlExec:
> > > > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > > > >     SET
> > > > > > > > 	end_time = SYSDATE,
> > > > > > > > 	row_alg_invocation_id = ?,
> > > > > > > > 	modification_date = SYSDATE
> > > > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > > > >   bindValues (167, 167)
> > > > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > Michael Luchtan
> > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > >
> > > > > > > >
> > > > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > > > >
> > > > > > > > > Hey Michael,
> > > > > > > > >
> > > > > > > > > Can you run it again with the --verbose flag set, and resend the output?
> > > > > > > > > That will probably help me figure out the error much easier.  Thanks,
> > > > > > > > >
> > > > > > > > > Dave
> > > > > > > > >
> > > > > > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > > > > > >
> > > > > > > > > > Hello Dave-
> > > > > > > > > > Here is the error:
> > > > > > > > > >
> > > > > > > > > > [luchtan@mango gbparserFailures]$ ga
> > > > > > > > > > GUS::GOPredict::Plugin::LoadGoOntology --create_release
> > > > > > > > > > --file_path=/home/gusdev/gus3.0-checkouts/GO --id_file=/home/luchtan/GOLOG
> > > > > > > > > >
> > > > > > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > Thu May 15 00:48:36 2003	loading all .ontology files in
> > > > > > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > > > > > Thu May 15 00:48:36 2003	parsing all .ontology files in preparation
> > > > > > > > > > for inserting into database
> > > > > > > > > > Thu May 15 00:48:44 2003	parsing finished; loading ontology into
> > > > > > > > > > database
> > > > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > > > prepareAndExecute FAILED:
> > > > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2150)->errstr
> > > > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > > > >
> > > > > > > > > > Some kind of referencing error?  Thanks,
> > > > > > > > > >
> > > > > > > > > > Michael Luchtan
> > > > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > -------------------------------------------------------
> > > > > > > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > > > > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > > > > > > www.enterpriselinuxforum.com
> > > > > > > > > >
> > > > > > > > > > _______________________________________________
> > > > > > > > > > Gusdev-gusdev mailing list
> > > > > > > > > > Gus...@li...
> > > > > > > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > The only event dedicated to issues related to Linux enterprise solutions
> > > www.enterpriselinuxforum.com
> > >
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> >
> >
> >
> > -------------------------------------------------------
> > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > The only event dedicated to issues related to Linux enterprise solutions
> > www.enterpriselinuxforum.com
> >
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
>

Re: [Gusdev-gusdev] database problem?

[Terry C. <tw...@gu...>]

Hi Michael,
Thanks for your comments and taking a shot at this.
I am working offline from the gus-dev list with help from Steve 
and others to get the UChicago GUS installation properly setup.  
Even with that and knowing there is work underway to make 
GUS use easier out of the gate, I decided to post this query 
because both messages occur during fresh installation of modules 
from PROJECT_HOME into GUS_HOME.

Terry



On  0, MICHAEL LUCHTAN <lu...@cs...> wrote:
> Hey-
> I'm kind of new to this GUS thing myself(a week or two), but I came in on
> an already set-up GUS schema.  I'm no DBA, but I guess I'll figure it out.
> We get the second type of error all the time.  I'm not sure what it means,
> but the person who set up the database here told me that it was
> ignorable-- Chetna, or anyone, can you explain what a roll-back error is?
> I think it is some kind of advanced configuration of Oracle.
> 
> As for the first error-- are those commit errors?  Do you know about
> registering the plug-ins with GUS?  Every plugin must be registered before
> it can be used.  Check out the archives, 'cuz Steve Fischer sent me an
> -email a couple of days ago about adding plug-ins.  I think the subject
> line was something like "meta, commit, and something".  But that's not
> enough for me to know what your first error is or if it is related to
> registering plug-ins.
> 
> Good Luck
> 
> 
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
> 
> 
> On Sat, 17 May 2003, Terry Clark wrote:
> 
> > I get the two messages below -- and understand neither --
> > both during fresh installation of GUS modules ("build GUS install -append")
> > and with "ga -history <plugin>". Our GUS configuration is incomplete,
> > but since this happens during installation,  I think it
> > may be worth understanding, at least to know if it is ignorable.
> > Could anyone help out with a comment or two about this?
> >
> > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup,
> > RootClass ignored at /home2/gus/run/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 147
> >
> > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation in
> > Automatic Undo mode (DBD ERROR: OCIStmtExecute) [for statement ``set transaction use
> > rollback segment BIGRBS1'']) at /home2/gus/run/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> >
> > Terry
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: If flattening out C++ or Java
> > code to make your application fit in a relational database is painful,
> > don't do it! Check out ObjectStore. Now part of Progress Software.
> > http://www.objectstore.net/sourceforge
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >

Re: [Gusdev-gusdev] database problem?

[MICHAEL L. <lu...@cs...>]

Hey-
I'm kind of new to this GUS thing myself(a week or two), but I came in on
an already set-up GUS schema.  I'm no DBA, but I guess I'll figure it out.
We get the second type of error all the time.  I'm not sure what it means,
but the person who set up the database here told me that it was
ignorable-- Chetna, or anyone, can you explain what a roll-back error is?
I think it is some kind of advanced configuration of Oracle.

As for the first error-- are those commit errors?  Do you know about
registering the plug-ins with GUS?  Every plugin must be registered before
it can be used.  Check out the archives, 'cuz Steve Fischer sent me an
-email a couple of days ago about adding plug-ins.  I think the subject
line was something like "meta, commit, and something".  But that's not
enough for me to know what your first error is or if it is related to
registering plug-ins.

Good Luck


Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Sat, 17 May 2003, Terry Clark wrote:

> I get the two messages below -- and understand neither --
> both during fresh installation of GUS modules ("build GUS install -append")
> and with "ga -history <plugin>". Our GUS configuration is incomplete,
> but since this happens during installation,  I think it
> may be worth understanding, at least to know if it is ignorable.
> Could anyone help out with a comment or two about this?
>
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup,
> RootClass ignored at /home2/gus/run/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 147
>
> DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation in
> Automatic Undo mode (DBD ERROR: OCIStmtExecute) [for statement ``set transaction use
> rollback segment BIGRBS1'']) at /home2/gus/run/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
>
> Terry
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: If flattening out C++ or Java
> code to make your application fit in a relational database is painful,
> don't do it! Check out ObjectStore. Now part of Progress Software.
> http://www.objectstore.net/sourceforge
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] database problem?

[Terry C. <tw...@gu...>]

I get the two messages below -- and understand neither --
both during fresh installation of GUS modules ("build GUS install -append")
and with "ga -history <plugin>". Our GUS configuration is incomplete, 
but since this happens during installation,  I think it 
may be worth understanding, at least to know if it is ignorable. 
Could anyone help out with a comment or two about this?

DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, 
RootClass ignored at /home2/gus/run/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 147

DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation in 
Automatic Undo mode (DBD ERROR: OCIStmtExecute) [for statement ``set transaction use 
rollback segment BIGRBS1'']) at /home2/gus/run/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.

Terry

[Gusdev-gusdev] web applications

[Terry C. <tw...@gu...>]

Hi All,

We here at the University of Chicago are working 
our GUS development strategy to incorporate, early,
web-interface front ends. A first task we would like 
to perform is to install the schema browser; then
we'd like to develop contemporaneously with our other
GUS work simple, web-based interfaces to poke and probe 
GUS content.

Can we get some current source for some/any web tool
development (partially) current with GUS 3.0?  Is there
a schema browser that works with the current GUS
release? (We have the posted schema browser source.) 
We're willing and able to work with partial solutions, 
which I expect is preferable to working from scratch.

Thanks in advance for any advice!

Terry

Re: [Gusdev-gusdev] Load GOOntology error--

[MICHAEL L. <lu...@cs...>]

Hello-
The code needs to be changed not only on line 500, but also line 474:
    my $branchGoTerm = GUS::Model::SRes::GOTerm->new({
	go_id  => $ancestorGoId,
	external_database_release_id => $extDbRelId,
	source_id => $branchRootEntry->getId(),
	name  => $branchRootEntry->getName(), #just the name
	definition   => $branchRootEntry->getName(),
	minimum_level => 1,
	maximum_level => 1,
	number_of_levels => 1,
#	ancestor_go_term_id => $tempGusId,

But unfortunately, this did not solve the problem.  From what I can gather
of the following log, the allowing of NULL into the ancestor_go_term_id
causes another error in GORelationship.  I imagine that this table, too,
can be modified, but wanted some feedback before going through with this.
How big a problem do you think it will cause to allow ancestor_go_term_id
in table sres.goterm to be NULL?
Here is the log:
[luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
--create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
--id_file=/home/luchtan/GOLOG --verbose
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.


prepareAndExecute:     SELECT *
      FROM Core.AlgorithmImplementation
     WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
       AND cvs_revision    = '1.11.2'


DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.


prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t,
Core.DatabaseInfo d where d.database_id = t.database_id
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.

RetrieveFromDB: select * from Core.AlgorithmImplementation where
algorithm_implementation_id = ?
  bindValues (92)


prepareAndExecute: select login,user_id from Core.UserInfo


prepareAndExecute: select name,group_id from Core.GroupInfo


prepareAndExecute: select name,project_id from Core.ProjectInfo


sqlExec:
    INSERT INTO Core.AlgorithmInvocation (  end_time, row_user_id,
user_write, group_write, cpu_time, algorithm_implementation_id,
row_project_id, algorithm_invocation_id, comment_string, group_read,
row_group_id, result, other_read, cpus_used, start_time,
modification_date, user_read, row_alg_invocation_id, other_write,
machine_id )
    VALUES   (  SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, SYSDATE,
SYSDATE, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 92, 2, 176, 1, 3, pending, 1, 1, 1, 1, 0, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKey where
algorithm_implementation_id = ?
  bindValues (92)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (2)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
)
  bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1795, 345, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (0)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1796, 346, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (4)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1797, 357, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1798, 349, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1799, 353, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
)
  bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1800, 347, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/gusdev/gus3.0-checkouts/GO,
3, 1, 1, 176, 1801, 356, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1802, 360, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1803, 354, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1804, 344, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1805, 359, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/gus.properties, 3,
1, 1, 176, 1806, 343, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/GOLOG, 3, 1, 1, 176,
1807, 352, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1808, 358, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1809, 351, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1810, 348, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1811, 350, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1812, 355, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
executing Select external_database_id from sres.externaldatabase where
name = ? GO Function
executing Select external_database_id from sres.externaldatabase where
name = ? GO Component
executing Select external_database_id from sres.externaldatabase where
name = ? GO Process
Fri May 16 01:07:22 2003	loading all .ontology files in
/home/gusdev/gus3.0-checkouts/GO in preparation for parsing
Fri May 16 01:07:22 2003	parsing all .ontology files in preparation
for inserting into database
Fri May 16 01:07:31 2003	parsing finished; loading ontology into
database


prepareAndExecute: select external_database_release_id
               from sres.externalDatabaseRelease
               where version = '2.690' and external_database_id = 92


sqlExec:
    INSERT INTO SRes.ExternalDatabaseRelease (  row_user_id, other_read,
user_write, group_write, external_database_id, row_project_id,
modification_date, user_read, external_database_release_id,
row_alg_invocation_id, group_read, version, other_write, row_group_id )
    VALUES   (  ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 1, 92, 2, 1, 95, 176, 1, 2.690, 0, 3)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Fri May 16 01:07:31 2003	successfully submitted new entry into
SRes.ExternalDatabaseReleaseId with primary key of 95

Fri May 16 01:07:31 2003	making root node for function


sqlExec:
    INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write,
group_write, row_project_id, name, external_database_release_id,
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, other_write, definition )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?,
?, ?, ? )
  bindValues (6, GO:0003674, 1, 1, 2, molecular_function, 95, 1, 1, 3, 6,
1, GO:0003674, 1, 176, 1, 1, 0, molecular_function)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


prepareAndExecute: Update SRes.GOTerm Set ancestor_go_term_id = 6
               where external_database_release_id = 95
               and go_term_id = 6
Fri May 16 01:07:31 2003	loading GO Terms into SRes.GOTerm


prepareAndExecute: select go_relationship_type_id, name
               from sres.gorelationshiptype
Fri May 16 01:07:31 2003	loading hierarchy and synonyms into
SRes.GORelationship and SRes.GOSynonym


sqlExec:
    INSERT INTO SRes.GORelationship (  row_user_id, other_read,
user_write, group_write, child_term_id, row_project_id,
go_relationship_id, modification_date, go_relationship_type_id, user_read,
row_alg_invocation_id, group_read, parent_term_id, other_write,
row_group_id )
    VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
  bindValues (6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3)
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("SRES"."GORELATIONSHIP"."PARENT_TERM_ID") (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (176, 176)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

 SQL ERROR!! involving

    INSERT INTO SRes.GORelationship (  row_user_id, other_read,
user_write, group_write, child_term_id, row_project_id,
go_relationship_id, modification_date, go_relationship_type_id, user_read,
row_alg_invocation_id, group_read, parent_term_id, other_write,
row_group_id )
    VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
 Values: 6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3 at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
'^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GORelationship ( ...')
called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8b73214)', 'ARRAY(0x8b73298)', '^J
INSERT INTO SRes.GORelationship (  row_user_id, other_read,...') called at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)',
'HASH(0x896950c)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 621

GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677

GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
line 271

GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ceb4)') called at
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144

GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
'HASH(0x882ce84)') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
	eval {...} called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::GOPredict::Plugin::LoadGoOntology') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::GOPredict::Plugin::LoadGoOntology') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11


Thanks,

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Fri, 16 May 2003, Dave Barkan wrote:

> Hi Michael and folks,
>
> This is the result of a known bug in the database schema.  Right now,
> there is a non-nullable foreign key in SRes.GoTerm that points back to
> SRes.GoTerm itself (the foreign key being ancestor_go_term).
>
> I believe I submitted a request for a schema change, but until that change
> is implemented the temporary solution is a hack; when loading the root
> term of the GO Ontology, I just set the ancestor_go_term to 1, so that it
> temporarily points to whatever entry is in SRes.GoTerm with an ID of 1.
> Then I immediately update the root entry to (correctly) point to itself as
> the ancestor_go_term.
>
> However, since you are loading the Ontology for the first time, you
> obviously won't have any entry with an ID of 1; that is the cause of the
> error message you are getting.
>
> I think the only solution to this is to make the column ancestor_go_term
> nullable.  After that, you will have to take out the line in the plugin
> that does that does the hack of setting the ancestor_go_term to 1, which
> is shown here:
>
> (line 500 of LoadGoOntology.pm):
>
>  my $ontologyGoTerm = GUS::Model::SRes::GOTerm->new({
> 	go_id  => $rootGoId,
> 	external_database_release_id => $extDbRelId,
> 	source_id => $rootEntry->getId(),
> 	name  => $rootEntry->getName(), #just the name
> 	definition   => $rootEntry->getName(),
> 	minimum_level => 0,
> 	maximum_level => 0,
> 	number_of_levels => 1,
> 	ancestor_go_term_id => $tempAncestorId,  #remove this line
>     } );
>
> After reading some of the previous email traffic on the gus-dev list, I'm
> not sure if you have permissions to make these modifications.  I can make
> them for you and resubmit them to cvs, but I am hesitant to make this
> change permanent until we have the schema change to make the column
> non-nullable instituted in our copy of GUS.  This brings up some of the
> larger questions about how schema changes to GUS are ensured to remain
> consistent among all copies of GUS. I'm sure there's a protocol; while I'm
> not familiar with it I'm sure other people on this list are and could
> help you out implementing all of this.
>
> Glad you got the plugin running; did you end up passing in the external
> database ids as command line parameters or did you figure out what was
> causing the previous problem some other way?
>
> Dave
>
>
>
> On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:
>
> > Dave-
> > Check it out:
> > [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > --id_file=/home/luchtan/GOLOG --verbose
> > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > Reading properties from /home/luchtan/gus.properties
> > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
>
>
> > executing Select external_database_id from sres.externaldatabase where
> > name = ? GO Function
> > executing Select external_database_id from sres.externaldatabase where
> > name = ? GO Component
> > executing Select external_database_id from sres.externaldatabase where
> > name = ? GO Process
> > Thu May 15 23:59:40 2003	loading all .ontology files in
> > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > Thu May 15 23:59:40 2003	parsing all .ontology files in preparation
> > for inserting into database
> > Thu May 15 23:59:49 2003	parsing finished; loading ontology into
> > database
> >
> >
> > prepareAndExecute: select external_database_release_id
> >                from sres.externalDatabaseRelease
> >                where version = '2.690' and external_database_id = 92
> >
>
> > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology)
> > DBD::Oracle::st execute failed: ORA-02291: integrity constraint
> > (SRES.GOTERM_FK02) violated - parent key not found (DBD ERROR:
> > OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
> > 144.
> >
> >
> > sqlExec:
> >     UPDATE  Core.AlgorithmInvocation
> >     SET
> > 	end_time = SYSDATE,
> > 	row_alg_invocation_id = ?,
> > 	modification_date = SYSDATE
> >     WHERE   algorithm_invocation_id = ?
> >   bindValues (174, 174)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >  SQL ERROR!! involving
> >
> >     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, 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, other_write,
> > definition )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
> > ?, ?, ?, ? )
> >  Values: 6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
> > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> >
> > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GOTerm (  row_use...')
> > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> >
> > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8bc753c)', 'ARRAY(0x8bc75c0)', '^J
> > INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, ...') called at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> >
> > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)',
> > 'HASH(0x890dc40)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > line 621
> >
> > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >
> > GUS::Model::GusRow::submit('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > line 512
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::__makeOntologyRoot('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > 'HASH(0x8e7c514)', 'GO:0003673', 93) called at
> > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 437
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::__makeRoots('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > 'HASH(0x8e7c514)', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x8b26f04)',
> > 93, undef, 'FileHandle=GLOB(0x88c801c)') called at
> > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 195
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ce64)') called at
> > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > 'HASH(0x882ce34)') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > 	eval {...} called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> >
> > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> >
> > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> >
> > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> >
> >
> > Looks like an sql error, but I'm not sure what to do about it.  Do any of
> > the rror messages give you any leads?
> >
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> > On Thu, 15 May 2003, Dave Barkan wrote:
> >
> > > Hey Michael,
> > >
> > > I still think that the error is an sql error.  It does say
> > >
> > > > Can't call method "execute" without a package or object reference at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > >
> > > but my experience is that that message is printed out when the sql
> > > statement is not what it expects.  The fact that it also says
> > >
> > >  prepareAndExecute: select external_database_release_id
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.690' and external_database_id =
> > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > >
> > > and doesn't print out the external_database_id in the statement is why I
> > > am focusing on the external database issue.  Here's what I did so we can
> > > narrow it down:
> > >
> > > 1.  I added an error statement if the plugin tries to run this query and
> > > can't find the database id; that way we can be sure about the problem.
> > >
> > > 2.  I added three command line arguments: function_db_id, process_db_id,
> > > and component_db_id.  You can pass these in to specify the external
> > > database ids of the respective branches, thus avoiding the
> > > programming hack of hardcoded entries in the database.
> > >
> > > To rerun, just do the following:
> > >
> > > 1. cvs update LoadGoOntology to get the version I just committed.
> > > 2. run 'build GUS/GOPredict install -append' to build the plugin.
> > > 3. run the command 'ga +update GUS::GOPredict::Plugin::LoadGoOntology
> > > --commit'
> > >
> > > (this sequence of commands generally has to be done whenever changes have
> > > been made to a plugin, especially those to the command line arguments).
> > >
> > > Try that, run it with the --verbose flag set, and let me know what you
> > > see.
> > >
> > > Dave
> > >
> > >
> > >
> > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > >
> > > > Dave-
> > > >
> > > > Yes, we ran the provided queries, and they are in the table.  Also, those
> > > > files are there as downloaded from the ftp site that you provided.
> > > > Again, here is a snapshot of where it failed(which seems more like a
> > > > compiler error than an sql error):
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 169, 1, 3, 1, 1, 169, 1740, 304, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > Thu May 15 03:01:35 2003	loading all .ontology files in
> > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > Thu May 15 03:01:35 2003	parsing all .ontology files in preparation
> > > > for inserting into database
> > > > Thu May 15 03:01:43 2003	parsing finished; loading ontology into
> > > > database
> > > >
> > > >
> > > > prepareAndExecute: select external_database_release_id
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.690' and external_database_id =
> > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > prepareAndExecute FAILED:
> > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2074)->errstr
> > > >
> > > >
> > > > sqlExec:
> > > >     UPDATE  Core.AlgorithmInvocation
> > > >     SET
> > > > 	end_time = SYSDATE,
> > > > 	row_alg_invocation_id = ?,
> > > > 	modification_date = SYSDATE
> > > >     WHERE   algorithm_invocation_id = ?
> > > >   bindValues (169, 169)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > Can't call method "execute" without a package or object reference at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > >
> > > >
> > > > Thanks,
> > > >
> > > > Michael Luchtan
> > > > http://www.cs.uga.edu/~luchtan
> > > >
> > > >
> > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > >
> > > > > Hey Michael,
> > > > >
> > > > > Alright, I'm still not sure it isn't an issue with an external database
> > > > > entry.  Try these two things.
> > > > >
> > > > > 1.Run the query 'select external_database_id from sres.externaldatabase
> > > > > where name = ?'
> > > > >
> > > > > and substitute 'GO Function,' GO Process,' 'GO Component' for each ?.
> > > > >
> > > > > 2. Make sure that the ontology files you are loading from are of the form
> > > > > 'branch.ontology' where branch can be one of 'process', 'function', or
> > > > > 'component.' These are the names of the files when they are downloaded
> > > > > from the GO site.
> > > > >
> > > > > The reason I want you to give the query a shot is that the plugin runs the
> > > > > same query to get the id's of those databases.  Then it turns around and
> > > > > uses those ids in the query that is failing:
> > > > >
> > > > > >
> > > > > > prepareAndExecute: select external_database_release_id
> > > > > >                from sres.externalDatabaseRelease
> > > > > >                where version = '2.690' and external_database_id =
> > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > >
> > > > > Sorry if this is overkill to try to figure this one out but I guess that's
> > > > > the disadvantage of debugging across state lines!
> > > > >
> > > > > dave
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > prepareAndExecute FAILED:
> > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2084)->errstr
> > > > > >
> > > > > >
> > > > > > sqlExec:
> > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > >     SET
> > > > > > 	end_time = SYSDATE,
> > > > > > 	row_alg_invocation_id = ?,
> > > > > > 	modification_date = SYSDATE
> > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > >   bindValues (167, 167)
> > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > Can't call method "execute" without a package or object reference at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > >
> > > > > >
> > > > > >
> > > > > > Michael Luchtan
> > > > > > http://www.cs.uga.edu/~luchtan
> > > > > >
> > > > > >
> > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > >
> > > > > > > Hey Michael,
> > > > > > >
> > > > > > > Can you run it again with the --verbose flag set, and resend the output?
> > > > > > > That will probably help me figure out the error much easier.  Thanks,
> > > > > > >
> > > > > > > Dave
> > > > > > >
> > > > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > > > >
> > > > > > > > Hello Dave-
> > > > > > > > Here is the error:
> > > > > > > >
> > > > > > > > [luchtan@mango gbparserFailures]$ ga
> > > > > > > > GUS::GOPredict::Plugin::LoadGoOntology --create_release
> > > > > > > > --file_path=/home/gusdev/gus3.0-checkouts/GO --id_file=/home/luchtan/GOLOG
> > > > > > > >
> > > > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > Thu May 15 00:48:36 2003	loading all .ontology files in
> > > > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > > > Thu May 15 00:48:36 2003	parsing all .ontology files in preparation
> > > > > > > > for inserting into database
> > > > > > > > Thu May 15 00:48:44 2003	parsing finished; loading ontology into
> > > > > > > > database
> > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > prepareAndExecute FAILED:
> > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2150)->errstr
> > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > >
> > > > > > > > Some kind of referencing error?  Thanks,
> > > > > > > >
> > > > > > > > Michael Luchtan
> > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > -------------------------------------------------------
> > > > > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > > > > www.enterpriselinuxforum.com
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > Gusdev-gusdev mailing list
> > > > > > > > Gus...@li...
> > > > > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>
>
> -------------------------------------------------------
> Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> The only event dedicated to issues related to Linux enterprise solutions
> www.enterpriselinuxforum.com
>
> _______________________________________________
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>

Re: [Gusdev-gusdev] meta, update, commit, etc...

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

Michael-

you should only need to run +meta iff GusApplication.pm has changed.

stefe

MICHAEL LUCHTAN wrote:

>Steve-
>Thanks... Concating to  the cvs revision number in the code is how we
>got around the previous problem with GBParser.  I've got my original
>problem/plugin solved/working, but just as a clarification, how often do
>you need to run ga +meta --commit?  It seems everytime that I try to
>register a new plugin with +update --commit it tells me to run ga +meta
>--commit (but maybe that's because I tend to rebuild the whole tree).
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Fri, 16 May 2003, Steve Fischer wrote:
>
>  
>
>>Michael-
>>
>>Thanks for being persistent and I'm glad that at least so far there's a
>>DONT in your illustrative package name.
>>
>>Yes, it sounds like you got the build down.
>>
>>You have stumbled into what I think is the one remaining "known issue"
>>with ga:  it lets you do a 'ga +meta --commit' when it is not needed,
>>and that does cause an error that needs a minor cleanup.
>>
>>First let me explain what is going on with +update, +create and +meta.
>>
>>The basic idea is that these register a plugin version with the db.  ga
>>will not allow you to run an unregistered version of a plugin (unless
>>you do not use --commit).
>>
>>Use +create when you want to register a plugin with your GUS db for the
>>first time.  This would happen when you first run a plugin at your site.
>>
>>Use +update when you want to run a version of a plugin that is more
>>recent then the one that is registered in your database.  This would
>>happen if:
>>  1. you have installed a new version of the gus software (eg, gotten a
>>new version from cvs), or
>>  2. you have:
>>      a. edited a plugin,
>>      b. cvs checked it in,
>>      c. run the build system
>>
>>
>>This informs the db of the new version of the plugin.
>>
>>Note that step 2 implies that you have developer access to the plugin
>>you are modifying.  For the plugins that are packaged with GUS I think
>>that your group does not have that access.  In other words, as it stands
>>right now, without developer rights, you shouldn't be able modify any of
>>the built-in plugins. Trying to do so should trigger an error when you
>>run ga.  (Which does lead to the question of how you guys were able to
>>hack in the date format change you told me about.  Which file did you
>>make that change in?).
>>
>>Use +meta when you have installed a new version of the GUS software, and
>>'ga' has been upgraded.
>>
>>Because I have not yet gotten the chance to fix ga so it prevents you
>>from running +meta more than once for a particular version of ga, you
>>will need to do a little trick to correct your db.
>>
>>Here is what to do to correct the problem of having run +meta more than
>>once for a given version of ga:
>>   1. edit $PROJECT_HOME/GUS/PluginMgr/lib/perl/GusApplication.pm
>>   2. find the line that looks like this:           cvsRevision =>
>>'$Revision: 1.37 $',
>>   3. what ever revision number is there, change it by adding a ".111"
>>on the end, thereby making it a unique version
>>   4. do a build GUS install -append
>>   5. run ga +meta --commit (only once!)
>>
>>Feel free to call (610) 649-8929
>>
>>steve
>>
>>
>>MICHAEL LUCHTAN wrote:
>>
>>    
>>
>>>Hello all-
>>>I am just getting started with gus, and was wondering if I could get a
>>>little guidence with regards to the versioning system.
>>>Correct me if I am wrong, but the following steps need to be taken when
>>>updating/installing a new module:
>>>1.  Get the module, and make sure that it is in the proper place in the
>>>directory tree.
>>>2.  Run build.
>>>
>>>I think I've got those down, but the next series of steps seem to be a
>>>jumble up.  I've tried all (two)possible permutations and all seem to
>>>grant some kind of error (for purpose of illustration, assume the plugin is
>>>GUS::BUS::DONT::Cuss):
>>>a. ga +update GUS::BUS::DONT::Cuss --commit
>>>b. ga +meta --commit
>>>
>>>Each one seems to require the other one, and if you do them more than
>>>once, you get an user error like:
>>>
>>>USER ERROR: Found more than one Core.AlgorithmImplementation for
>>>exe=GUS::PluginMgr::GusApplication cvsRev=1.37:
>>> algimp_id:87  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:
>>> algimp_id:83  md5:920905884ae1197584fccd39b294495b  rev:1.37  tag:
>>> algimp_id:88  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:
>>>
>>>And GUS::BUS::DONT::Cuss still doesn't work.
>>>So I have two questions:
>>>1.  What is the correct procedure?
>>>2.  How does one recover from the above error assuming you have executed
>>>statements a,b more than once.
>>>
>>>Michael Luchtan
>>>http://www.cs.uga.edu/~luchtan
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
>>>The only event dedicated to issues related to Linux enterprise solutions
>>>www.enterpriselinuxforum.com
>>>
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>      
>>>
>>    
>>
>
>
>
>-------------------------------------------------------
>Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
>The only event dedicated to issues related to Linux enterprise solutions
>www.enterpriselinuxforum.com
>
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] Load GOOntology error--

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

Hi Michael and folks,

This is the result of a known bug in the database schema.  Right now, 
there is a non-nullable foreign key in SRes.GoTerm that points back to 
SRes.GoTerm itself (the foreign key being ancestor_go_term).

I believe I submitted a request for a schema change, but until that change 
is implemented the temporary solution is a hack; when loading the root 
term of the GO Ontology, I just set the ancestor_go_term to 1, so that it 
temporarily points to whatever entry is in SRes.GoTerm with an ID of 1.  
Then I immediately update the root entry to (correctly) point to itself as 
the ancestor_go_term.

However, since you are loading the Ontology for the first time, you 
obviously won't have any entry with an ID of 1; that is the cause of the 
error message you are getting. 

I think the only solution to this is to make the column ancestor_go_term 
nullable.  After that, you will have to take out the line in the plugin 
that does that does the hack of setting the ancestor_go_term to 1, which 
is shown here:

(line 500 of LoadGoOntology.pm):

 my $ontologyGoTerm = GUS::Model::SRes::GOTerm->new({
	go_id  => $rootGoId, 
	external_database_release_id => $extDbRelId,
	source_id => $rootEntry->getId(), 
	name  => $rootEntry->getName(), #just the name
	definition   => $rootEntry->getName(),
	minimum_level => 0,
	maximum_level => 0,
	number_of_levels => 1,
	ancestor_go_term_id => $tempAncestorId,  #remove this line
    } );

After reading some of the previous email traffic on the gus-dev list, I'm 
not sure if you have permissions to make these modifications.  I can make 
them for you and resubmit them to cvs, but I am hesitant to make this 
change permanent until we have the schema change to make the column 
non-nullable instituted in our copy of GUS.  This brings up some of the 
larger questions about how schema changes to GUS are ensured to remain 
consistent among all copies of GUS. I'm sure there's a protocol; while I'm 
not familiar with it I'm sure other people on this list are and could 
help you out implementing all of this.

Glad you got the plugin running; did you end up passing in the external 
database ids as command line parameters or did you figure out what was 
causing the previous problem some other way?

Dave



On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:

> Dave-
> Check it out:
> [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> --id_file=/home/luchtan/GOLOG --verbose
> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> Reading properties from /home/luchtan/gus.properties
> DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.


> executing Select external_database_id from sres.externaldatabase where
> name = ? GO Function
> executing Select external_database_id from sres.externaldatabase where
> name = ? GO Component
> executing Select external_database_id from sres.externaldatabase where
> name = ? GO Process
> Thu May 15 23:59:40 2003	loading all .ontology files in
> /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> Thu May 15 23:59:40 2003	parsing all .ontology files in preparation
> for inserting into database
> Thu May 15 23:59:49 2003	parsing finished; loading ontology into
> database
> 
> 
> prepareAndExecute: select external_database_release_id
>                from sres.externalDatabaseRelease
>                where version = '2.690' and external_database_id = 92
> 

> GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology)
> DBD::Oracle::st execute failed: ORA-02291: integrity constraint
> (SRES.GOTERM_FK02) violated - parent key not found (DBD ERROR:
> OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
> 144.
> 
> 
> sqlExec:
>     UPDATE  Core.AlgorithmInvocation
>     SET
> 	end_time = SYSDATE,
> 	row_alg_invocation_id = ?,
> 	modification_date = SYSDATE
>     WHERE   algorithm_invocation_id = ?
>   bindValues (174, 174)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
>  SQL ERROR!! involving
> 
>     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, 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, other_write,
> definition )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
> ?, ?, ?, ? )
>  Values: 6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
> GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology at
> /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> 
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GOTerm (  row_use...')
> called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> 
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8bc753c)', 'ARRAY(0x8bc75c0)', '^J
> INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, ...') called at
> /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> 
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)',
> 'HASH(0x890dc40)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> line 621
> 
> GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> 
> GUS::Model::GusRow::submit('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> line 512
> 
> GUS::GOPredict::Plugin::LoadGoOntology::__makeOntologyRoot('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> 'HASH(0x8e7c514)', 'GO:0003673', 93) called at
> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 437
> 
> GUS::GOPredict::Plugin::LoadGoOntology::__makeRoots('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> 'HASH(0x8e7c514)', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x8b26f04)',
> 93, undef, 'FileHandle=GLOB(0x88c801c)') called at
> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 195
> 
> GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ce64)') called at
> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> 
> GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> 'HASH(0x882ce34)') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> 	eval {...} called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> 
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> 
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> 
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> 
> 
> Looks like an sql error, but I'm not sure what to do about it.  Do any of
> the rror messages give you any leads?
> 
> 
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
> 
> 
> On Thu, 15 May 2003, Dave Barkan wrote:
> 
> > Hey Michael,
> >
> > I still think that the error is an sql error.  It does say
> >
> > > Can't call method "execute" without a package or object reference at
> > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> >
> > but my experience is that that message is printed out when the sql
> > statement is not what it expects.  The fact that it also says
> >
> >  prepareAndExecute: select external_database_release_id
> > >                from sres.externalDatabaseRelease
> > >                where version = '2.690' and external_database_id =
> > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> >
> > and doesn't print out the external_database_id in the statement is why I
> > am focusing on the external database issue.  Here's what I did so we can
> > narrow it down:
> >
> > 1.  I added an error statement if the plugin tries to run this query and
> > can't find the database id; that way we can be sure about the problem.
> >
> > 2.  I added three command line arguments: function_db_id, process_db_id,
> > and component_db_id.  You can pass these in to specify the external
> > database ids of the respective branches, thus avoiding the
> > programming hack of hardcoded entries in the database.
> >
> > To rerun, just do the following:
> >
> > 1. cvs update LoadGoOntology to get the version I just committed.
> > 2. run 'build GUS/GOPredict install -append' to build the plugin.
> > 3. run the command 'ga +update GUS::GOPredict::Plugin::LoadGoOntology
> > --commit'
> >
> > (this sequence of commands generally has to be done whenever changes have
> > been made to a plugin, especially those to the command line arguments).
> >
> > Try that, run it with the --verbose flag set, and let me know what you
> > see.
> >
> > Dave
> >
> >
> >
> > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> >
> > > Dave-
> > >
> > > Yes, we ran the provided queries, and they are in the table.  Also, those
> > > files are there as downloaded from the ftp site that you provided.
> > > Again, here is a snapshot of where it failed(which seems more like a
> > > compiler error than an sql error):
> > >
> > > sqlExec:
> > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > group_write, is_default, order_num, row_project_id,
> > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > algorithm_param_id, algorithm_param_key_id, other_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > >   bindValues (6, 1, 1, 0, 0, 2, 169, 1, 3, 1, 1, 169, 1740, 304, 0)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > Thu May 15 03:01:35 2003	loading all .ontology files in
> > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > Thu May 15 03:01:35 2003	parsing all .ontology files in preparation
> > > for inserting into database
> > > Thu May 15 03:01:43 2003	parsing finished; loading ontology into
> > > database
> > >
> > >
> > > prepareAndExecute: select external_database_release_id
> > >                from sres.externalDatabaseRelease
> > >                where version = '2.690' and external_database_id =
> > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > prepareAndExecute FAILED:
> > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2074)->errstr
> > >
> > >
> > > sqlExec:
> > >     UPDATE  Core.AlgorithmInvocation
> > >     SET
> > > 	end_time = SYSDATE,
> > > 	row_alg_invocation_id = ?,
> > > 	modification_date = SYSDATE
> > >     WHERE   algorithm_invocation_id = ?
> > >   bindValues (169, 169)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > Can't call method "execute" without a package or object reference at
> > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > >
> > >
> > > Thanks,
> > >
> > > Michael Luchtan
> > > http://www.cs.uga.edu/~luchtan
> > >
> > >
> > > On Thu, 15 May 2003, Dave Barkan wrote:
> > >
> > > > Hey Michael,
> > > >
> > > > Alright, I'm still not sure it isn't an issue with an external database
> > > > entry.  Try these two things.
> > > >
> > > > 1.Run the query 'select external_database_id from sres.externaldatabase
> > > > where name = ?'
> > > >
> > > > and substitute 'GO Function,' GO Process,' 'GO Component' for each ?.
> > > >
> > > > 2. Make sure that the ontology files you are loading from are of the form
> > > > 'branch.ontology' where branch can be one of 'process', 'function', or
> > > > 'component.' These are the names of the files when they are downloaded
> > > > from the GO site.
> > > >
> > > > The reason I want you to give the query a shot is that the plugin runs the
> > > > same query to get the id's of those databases.  Then it turns around and
> > > > uses those ids in the query that is failing:
> > > >
> > > > >
> > > > > prepareAndExecute: select external_database_release_id
> > > > >                from sres.externalDatabaseRelease
> > > > >                where version = '2.690' and external_database_id =
> > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > >
> > > > Sorry if this is overkill to try to figure this one out but I guess that's
> > > > the disadvantage of debugging across state lines!
> > > >
> > > > dave
> > > >
> > > >
> > > >
> > > >
> > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > prepareAndExecute FAILED:
> > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2084)->errstr
> > > > >
> > > > >
> > > > > sqlExec:
> > > > >     UPDATE  Core.AlgorithmInvocation
> > > > >     SET
> > > > > 	end_time = SYSDATE,
> > > > > 	row_alg_invocation_id = ?,
> > > > > 	modification_date = SYSDATE
> > > > >     WHERE   algorithm_invocation_id = ?
> > > > >   bindValues (167, 167)
> > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > Can't call method "execute" without a package or object reference at
> > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > >
> > > > >
> > > > >
> > > > > Michael Luchtan
> > > > > http://www.cs.uga.edu/~luchtan
> > > > >
> > > > >
> > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > >
> > > > > > Hey Michael,
> > > > > >
> > > > > > Can you run it again with the --verbose flag set, and resend the output?
> > > > > > That will probably help me figure out the error much easier.  Thanks,
> > > > > >
> > > > > > Dave
> > > > > >
> > > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > > >
> > > > > > > Hello Dave-
> > > > > > > Here is the error:
> > > > > > >
> > > > > > > [luchtan@mango gbparserFailures]$ ga
> > > > > > > GUS::GOPredict::Plugin::LoadGoOntology --create_release
> > > > > > > --file_path=/home/gusdev/gus3.0-checkouts/GO --id_file=/home/luchtan/GOLOG
> > > > > > >
> > > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > Thu May 15 00:48:36 2003	loading all .ontology files in
> > > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > > Thu May 15 00:48:36 2003	parsing all .ontology files in preparation
> > > > > > > for inserting into database
> > > > > > > Thu May 15 00:48:44 2003	parsing finished; loading ontology into
> > > > > > > database
> > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > prepareAndExecute FAILED:
> > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2150)->errstr
> > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > >
> > > > > > > Some kind of referencing error?  Thanks,
> > > > > > >
> > > > > > > Michael Luchtan
> > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > -------------------------------------------------------
> > > > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > > > www.enterpriselinuxforum.com
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > Gusdev-gusdev mailing list
> > > > > > > Gus...@li...
> > > > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
> 

Re: [Gusdev-gusdev] Load GOOntology error--

[MICHAEL L. <lu...@cs...>]

Dave-
Check it out:
[luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
--create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
--id_file=/home/luchtan/GOLOG --verbose
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.


prepareAndExecute:     SELECT *
      FROM Core.AlgorithmImplementation
     WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
       AND cvs_revision    = '1.11'


DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.


prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t,
Core.DatabaseInfo d where d.database_id = t.database_id
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.

RetrieveFromDB: select * from Core.AlgorithmImplementation where
algorithm_implementation_id = ?
  bindValues (90)


prepareAndExecute: select login,user_id from Core.UserInfo


prepareAndExecute: select name,group_id from Core.GroupInfo


prepareAndExecute: select name,project_id from Core.ProjectInfo


sqlExec:
    INSERT INTO Core.AlgorithmInvocation (  end_time, row_user_id,
user_write, group_write, cpu_time, algorithm_implementation_id,
row_project_id, algorithm_invocation_id, comment_string, group_read,
row_group_id, result, other_read, cpus_used, start_time,
modification_date, user_read, row_alg_invocation_id, other_write,
machine_id )
    VALUES   (  SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, SYSDATE,
SYSDATE, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 90, 2, 174, 1, 3, pending, 1, 1, 1, 1, 0, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKey where
algorithm_implementation_id = ?
  bindValues (90)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (2)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
)
  bindValues (6, 1, 1, 0, 0, 2, 1, 174, 1, 1, 3, 1, 1, 174, 1759, 307, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (0)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1760, 315, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (4)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1761, 309, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1762, 320, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1763, 317, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
)
  bindValues (6, 1, 1, 0, 0, 2, 1, 174, 1, 1, 3, 1, 1, 174, 1764, 310, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, /home/gusdev/gus3.0-checkouts/GO,
3, 1, 1, 174, 1765, 318, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1766, 321, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1767, 313, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1768, 324, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1769, 316, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, /home/luchtan/gus.properties, 3,
1, 1, 174, 1770, 308, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, /home/luchtan/GOLOG, 3, 1, 1, 174,
1771, 323, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1772, 312, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1773, 319, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1774, 322, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1775, 314, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 174, 1, 3, 1, 1, 174, 1776, 311, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
executing Select external_database_id from sres.externaldatabase where
name = ? GO Function
executing Select external_database_id from sres.externaldatabase where
name = ? GO Component
executing Select external_database_id from sres.externaldatabase where
name = ? GO Process
Thu May 15 23:59:40 2003	loading all .ontology files in
/home/gusdev/gus3.0-checkouts/GO in preparation for parsing
Thu May 15 23:59:40 2003	parsing all .ontology files in preparation
for inserting into database
Thu May 15 23:59:49 2003	parsing finished; loading ontology into
database


prepareAndExecute: select external_database_release_id
               from sres.externalDatabaseRelease
               where version = '2.690' and external_database_id = 92


sqlExec:
    INSERT INTO SRes.ExternalDatabaseRelease (  row_user_id, other_read,
user_write, group_write, external_database_id, row_project_id,
modification_date, user_read, external_database_release_id,
row_alg_invocation_id, group_read, version, other_write, row_group_id )
    VALUES   (  ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 1, 92, 2, 1, 93, 174, 1, 2.690, 0, 3)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Thu May 15 23:59:49 2003	successfully submitted new entry into
SRes.ExternalDatabaseReleaseId with primary key of 93

Thu May 15 23:59:49 2003	making root node for function


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, 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, other_write,
definition )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
?, ?, ?, ? )
  bindValues (6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology)
DBD::Oracle::st execute failed: ORA-02291: integrity constraint
(SRES.GOTERM_FK02) violated - parent key not found (DBD ERROR:
OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
144.


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (174, 174)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

 SQL ERROR!! involving

    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, 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, other_write,
definition )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
?, ?, ?, ? )
 Values: 6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
'^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GOTerm (  row_use...')
called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8bc753c)', 'ARRAY(0x8bc75c0)', '^J
INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, ...') called at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)',
'HASH(0x890dc40)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 621

GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677

GUS::Model::GusRow::submit('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
line 512

GUS::GOPredict::Plugin::LoadGoOntology::__makeOntologyRoot('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
'HASH(0x8e7c514)', 'GO:0003673', 93) called at
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 437

GUS::GOPredict::Plugin::LoadGoOntology::__makeRoots('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
'HASH(0x8e7c514)', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x8b26f04)',
93, undef, 'FileHandle=GLOB(0x88c801c)') called at
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 195

GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ce64)') called at
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144

GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
'HASH(0x882ce34)') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
	eval {...} called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::GOPredict::Plugin::LoadGoOntology') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::GOPredict::Plugin::LoadGoOntology') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11


Looks like an sql error, but I'm not sure what to do about it.  Do any of
the rror messages give you any leads?


Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Thu, 15 May 2003, Dave Barkan wrote:

> Hey Michael,
>
> I still think that the error is an sql error.  It does say
>
> > Can't call method "execute" without a package or object reference at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
>
> but my experience is that that message is printed out when the sql
> statement is not what it expects.  The fact that it also says
>
>  prepareAndExecute: select external_database_release_id
> >                from sres.externalDatabaseRelease
> >                where version = '2.690' and external_database_id =
> > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
>
> and doesn't print out the external_database_id in the statement is why I
> am focusing on the external database issue.  Here's what I did so we can
> narrow it down:
>
> 1.  I added an error statement if the plugin tries to run this query and
> can't find the database id; that way we can be sure about the problem.
>
> 2.  I added three command line arguments: function_db_id, process_db_id,
> and component_db_id.  You can pass these in to specify the external
> database ids of the respective branches, thus avoiding the
> programming hack of hardcoded entries in the database.
>
> To rerun, just do the following:
>
> 1. cvs update LoadGoOntology to get the version I just committed.
> 2. run 'build GUS/GOPredict install -append' to build the plugin.
> 3. run the command 'ga +update GUS::GOPredict::Plugin::LoadGoOntology
> --commit'
>
> (this sequence of commands generally has to be done whenever changes have
> been made to a plugin, especially those to the command line arguments).
>
> Try that, run it with the --verbose flag set, and let me know what you
> see.
>
> Dave
>
>
>
> On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
>
> > Dave-
> >
> > Yes, we ran the provided queries, and they are in the table.  Also, those
> > files are there as downloaded from the ftp site that you provided.
> > Again, here is a snapshot of where it failed(which seems more like a
> > compiler error than an sql error):
> >
> > sqlExec:
> >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > group_write, is_default, order_num, row_project_id,
> > algorithm_invocation_id, group_read, string_value, row_group_id,
> > other_read, modification_date, user_read, row_alg_invocation_id,
> > algorithm_param_id, algorithm_param_key_id, other_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >   bindValues (6, 1, 1, 0, 0, 2, 169, 1, 3, 1, 1, 169, 1740, 304, 0)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > Thu May 15 03:01:35 2003	loading all .ontology files in
> > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > Thu May 15 03:01:35 2003	parsing all .ontology files in preparation
> > for inserting into database
> > Thu May 15 03:01:43 2003	parsing finished; loading ontology into
> > database
> >
> >
> > prepareAndExecute: select external_database_release_id
> >                from sres.externalDatabaseRelease
> >                where version = '2.690' and external_database_id =
> > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > (DBD ERROR: OCIStmtExecute/Describe) at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > prepareAndExecute FAILED:
> > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2074)->errstr
> >
> >
> > sqlExec:
> >     UPDATE  Core.AlgorithmInvocation
> >     SET
> > 	end_time = SYSDATE,
> > 	row_alg_invocation_id = ?,
> > 	modification_date = SYSDATE
> >     WHERE   algorithm_invocation_id = ?
> >   bindValues (169, 169)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > Can't call method "execute" without a package or object reference at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> >
> >
> > Thanks,
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> > On Thu, 15 May 2003, Dave Barkan wrote:
> >
> > > Hey Michael,
> > >
> > > Alright, I'm still not sure it isn't an issue with an external database
> > > entry.  Try these two things.
> > >
> > > 1.Run the query 'select external_database_id from sres.externaldatabase
> > > where name = ?'
> > >
> > > and substitute 'GO Function,' GO Process,' 'GO Component' for each ?.
> > >
> > > 2. Make sure that the ontology files you are loading from are of the form
> > > 'branch.ontology' where branch can be one of 'process', 'function', or
> > > 'component.' These are the names of the files when they are downloaded
> > > from the GO site.
> > >
> > > The reason I want you to give the query a shot is that the plugin runs the
> > > same query to get the id's of those databases.  Then it turns around and
> > > uses those ids in the query that is failing:
> > >
> > > >
> > > > prepareAndExecute: select external_database_release_id
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.690' and external_database_id =
> > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > >
> > > Sorry if this is overkill to try to figure this one out but I guess that's
> > > the disadvantage of debugging across state lines!
> > >
> > > dave
> > >
> > >
> > >
> > >
> > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > prepareAndExecute FAILED:
> > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2084)->errstr
> > > >
> > > >
> > > > sqlExec:
> > > >     UPDATE  Core.AlgorithmInvocation
> > > >     SET
> > > > 	end_time = SYSDATE,
> > > > 	row_alg_invocation_id = ?,
> > > > 	modification_date = SYSDATE
> > > >     WHERE   algorithm_invocation_id = ?
> > > >   bindValues (167, 167)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > Can't call method "execute" without a package or object reference at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > >
> > > >
> > > >
> > > > Michael Luchtan
> > > > http://www.cs.uga.edu/~luchtan
> > > >
> > > >
> > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > >
> > > > > Hey Michael,
> > > > >
> > > > > Can you run it again with the --verbose flag set, and resend the output?
> > > > > That will probably help me figure out the error much easier.  Thanks,
> > > > >
> > > > > Dave
> > > > >
> > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > >
> > > > > > Hello Dave-
> > > > > > Here is the error:
> > > > > >
> > > > > > [luchtan@mango gbparserFailures]$ ga
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology --create_release
> > > > > > --file_path=/home/gusdev/gus3.0-checkouts/GO --id_file=/home/luchtan/GOLOG
> > > > > >
> > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > Thu May 15 00:48:36 2003	loading all .ontology files in
> > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > Thu May 15 00:48:36 2003	parsing all .ontology files in preparation
> > > > > > for inserting into database
> > > > > > Thu May 15 00:48:44 2003	parsing finished; loading ontology into
> > > > > > database
> > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > prepareAndExecute FAILED:
> > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2150)->errstr
> > > > > > Can't call method "execute" without a package or object reference at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > >
> > > > > > Some kind of referencing error?  Thanks,
> > > > > >
> > > > > > Michael Luchtan
> > > > > > http://www.cs.uga.edu/~luchtan
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > -------------------------------------------------------
> > > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > > www.enterpriselinuxforum.com
> > > > > >
> > > > > > _______________________________________________
> > > > > > Gusdev-gusdev mailing list
> > > > > > Gus...@li...
> > > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>

Re: [Gusdev-gusdev] meta, update, commit, etc...

[MICHAEL L. <lu...@cs...>]

Steve-
Thanks... Concating to  the cvs revision number in the code is how we
got around the previous problem with GBParser.  I've got my original
problem/plugin solved/working, but just as a clarification, how often do
you need to run ga +meta --commit?  It seems everytime that I try to
register a new plugin with +update --commit it tells me to run ga +meta
--commit (but maybe that's because I tend to rebuild the whole tree).

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Fri, 16 May 2003, Steve Fischer wrote:

> Michael-
>
> Thanks for being persistent and I'm glad that at least so far there's a
> DONT in your illustrative package name.
>
> Yes, it sounds like you got the build down.
>
> You have stumbled into what I think is the one remaining "known issue"
> with ga:  it lets you do a 'ga +meta --commit' when it is not needed,
> and that does cause an error that needs a minor cleanup.
>
> First let me explain what is going on with +update, +create and +meta.
>
> The basic idea is that these register a plugin version with the db.  ga
> will not allow you to run an unregistered version of a plugin (unless
> you do not use --commit).
>
> Use +create when you want to register a plugin with your GUS db for the
> first time.  This would happen when you first run a plugin at your site.
>
> Use +update when you want to run a version of a plugin that is more
> recent then the one that is registered in your database.  This would
> happen if:
>   1. you have installed a new version of the gus software (eg, gotten a
> new version from cvs), or
>   2. you have:
>       a. edited a plugin,
>       b. cvs checked it in,
>       c. run the build system
>
>
> This informs the db of the new version of the plugin.
>
> Note that step 2 implies that you have developer access to the plugin
> you are modifying.  For the plugins that are packaged with GUS I think
> that your group does not have that access.  In other words, as it stands
> right now, without developer rights, you shouldn't be able modify any of
> the built-in plugins. Trying to do so should trigger an error when you
> run ga.  (Which does lead to the question of how you guys were able to
> hack in the date format change you told me about.  Which file did you
> make that change in?).
>
> Use +meta when you have installed a new version of the GUS software, and
> 'ga' has been upgraded.
>
> Because I have not yet gotten the chance to fix ga so it prevents you
> from running +meta more than once for a particular version of ga, you
> will need to do a little trick to correct your db.
>
> Here is what to do to correct the problem of having run +meta more than
> once for a given version of ga:
>    1. edit $PROJECT_HOME/GUS/PluginMgr/lib/perl/GusApplication.pm
>    2. find the line that looks like this:           cvsRevision =>
> '$Revision: 1.37 $',
>    3. what ever revision number is there, change it by adding a ".111"
> on the end, thereby making it a unique version
>    4. do a build GUS install -append
>    5. run ga +meta --commit (only once!)
>
> Feel free to call (610) 649-8929
>
> steve
>
>
> MICHAEL LUCHTAN wrote:
>
> >Hello all-
> >I am just getting started with gus, and was wondering if I could get a
> >little guidence with regards to the versioning system.
> >Correct me if I am wrong, but the following steps need to be taken when
> >updating/installing a new module:
> >1.  Get the module, and make sure that it is in the proper place in the
> >directory tree.
> >2.  Run build.
> >
> >I think I've got those down, but the next series of steps seem to be a
> >jumble up.  I've tried all (two)possible permutations and all seem to
> >grant some kind of error (for purpose of illustration, assume the plugin is
> >GUS::BUS::DONT::Cuss):
> >a. ga +update GUS::BUS::DONT::Cuss --commit
> >b. ga +meta --commit
> >
> >Each one seems to require the other one, and if you do them more than
> >once, you get an user error like:
> >
> >USER ERROR: Found more than one Core.AlgorithmImplementation for
> >exe=GUS::PluginMgr::GusApplication cvsRev=1.37:
> >  algimp_id:87  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:
> >  algimp_id:83  md5:920905884ae1197584fccd39b294495b  rev:1.37  tag:
> >  algimp_id:88  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:
> >
> >And GUS::BUS::DONT::Cuss still doesn't work.
> >So I have two questions:
> >1.  What is the correct procedure?
> >2.  How does one recover from the above error assuming you have executed
> >statements a,b more than once.
> >
> >Michael Luchtan
> >http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
> >-------------------------------------------------------
> >Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> >The only event dedicated to issues related to Linux enterprise solutions
> >www.enterpriselinuxforum.com
> >
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
>

Re: [Gusdev-gusdev] meta, update, commit, etc...

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

Michael-

Thanks for being persistent and I'm glad that at least so far there's a 
DONT in your illustrative package name.

Yes, it sounds like you got the build down.

You have stumbled into what I think is the one remaining "known issue" 
with ga:  it lets you do a 'ga +meta --commit' when it is not needed, 
and that does cause an error that needs a minor cleanup.  

First let me explain what is going on with +update, +create and +meta.

The basic idea is that these register a plugin version with the db.  ga 
will not allow you to run an unregistered version of a plugin (unless 
you do not use --commit).

Use +create when you want to register a plugin with your GUS db for the 
first time.  This would happen when you first run a plugin at your site.

Use +update when you want to run a version of a plugin that is more 
recent then the one that is registered in your database.  This would 
happen if:
  1. you have installed a new version of the gus software (eg, gotten a 
new version from cvs), or
  2. you have:
      a. edited a plugin,
      b. cvs checked it in,
      c. run the build system


This informs the db of the new version of the plugin.

Note that step 2 implies that you have developer access to the plugin 
you are modifying.  For the plugins that are packaged with GUS I think 
that your group does not have that access.  In other words, as it stands 
right now, without developer rights, you shouldn't be able modify any of 
the built-in plugins. Trying to do so should trigger an error when you 
run ga.  (Which does lead to the question of how you guys were able to 
hack in the date format change you told me about.  Which file did you 
make that change in?).

Use +meta when you have installed a new version of the GUS software, and 
'ga' has been upgraded.

Because I have not yet gotten the chance to fix ga so it prevents you 
from running +meta more than once for a particular version of ga, you 
will need to do a little trick to correct your db.  

Here is what to do to correct the problem of having run +meta more than 
once for a given version of ga:
   1. edit $PROJECT_HOME/GUS/PluginMgr/lib/perl/GusApplication.pm
   2. find the line that looks like this:           cvsRevision => 
'$Revision: 1.37 $',
   3. what ever revision number is there, change it by adding a ".111" 
on the end, thereby making it a unique version
   4. do a build GUS install -append
   5. run ga +meta --commit (only once!)

Feel free to call (610) 649-8929

steve


MICHAEL LUCHTAN wrote:

>Hello all-
>I am just getting started with gus, and was wondering if I could get a
>little guidence with regards to the versioning system.
>Correct me if I am wrong, but the following steps need to be taken when
>updating/installing a new module:
>1.  Get the module, and make sure that it is in the proper place in the
>directory tree.
>2.  Run build.
>
>I think I've got those down, but the next series of steps seem to be a
>jumble up.  I've tried all (two)possible permutations and all seem to
>grant some kind of error (for purpose of illustration, assume the plugin is
>GUS::BUS::DONT::Cuss):
>a. ga +update GUS::BUS::DONT::Cuss --commit
>b. ga +meta --commit
>
>Each one seems to require the other one, and if you do them more than
>once, you get an user error like:
>
>USER ERROR: Found more than one Core.AlgorithmImplementation for
>exe=GUS::PluginMgr::GusApplication cvsRev=1.37:
>  algimp_id:87  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:
>  algimp_id:83  md5:920905884ae1197584fccd39b294495b  rev:1.37  tag:
>  algimp_id:88  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:
>
>And GUS::BUS::DONT::Cuss still doesn't work.
>So I have two questions:
>1.  What is the correct procedure?
>2.  How does one recover from the above error assuming you have executed
>statements a,b more than once.
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>
>
>-------------------------------------------------------
>Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
>The only event dedicated to issues related to Linux enterprise solutions
>www.enterpriselinuxforum.com
>
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] meta, update, commit, etc...

[MICHAEL L. <lu...@cs...>]

Hello all-
I am just getting started with gus, and was wondering if I could get a
little guidence with regards to the versioning system.
Correct me if I am wrong, but the following steps need to be taken when
updating/installing a new module:
1.  Get the module, and make sure that it is in the proper place in the
directory tree.
2.  Run build.

I think I've got those down, but the next series of steps seem to be a
jumble up.  I've tried all (two)possible permutations and all seem to
grant some kind of error (for purpose of illustration, assume the plugin is
GUS::BUS::DONT::Cuss):
a. ga +update GUS::BUS::DONT::Cuss --commit
b. ga +meta --commit

Each one seems to require the other one, and if you do them more than
once, you get an user error like:

USER ERROR: Found more than one Core.AlgorithmImplementation for
exe=GUS::PluginMgr::GusApplication cvsRev=1.37:
  algimp_id:87  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:
  algimp_id:83  md5:920905884ae1197584fccd39b294495b  rev:1.37  tag:
  algimp_id:88  md5:d17ad6e0d94a36f54b6b91c11df00b76  rev:1.37  tag:

And GUS::BUS::DONT::Cuss still doesn't work.
So I have two questions:
1.  What is the correct procedure?
2.  How does one recover from the above error assuming you have executed
statements a,b more than once.

Michael Luchtan
http://www.cs.uga.edu/~luchtan