gusdev-gusdev — Topics concerning GUS development

[Gusdev-gusdev] Re: Error: subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, RootClass ignored at

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

yes, you can ignore these.

also, this has been fixed in the latest code in cvs.  the file to get is 
GUS/OblRelP/lib/perl/DbiDbHandle.pm

steve

Chetna Warade wrote:

>Hello All,
>
>While I am running ga +meta --commit or ga + create
>
>I getting this error:
>
>[chetna@mkiwi chetna]$  ga +create
>GUS::Common::Plugin::SubmitRow --commit
>Reading properties from
>/var/local/gus_home/config/GUS-PluginMgr.prop
>Reading properties from /home/chetna/.gus.properties
>GUS::ObjRelP::DbiDbHandle
>dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD chetna   0
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>GUS::ObjRelP::DbiDbHandle
>dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD chetna
>chetna123  0 1DBI subclasses
>'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
>setup, RootClass ignored at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>GUS::ObjRelP::DbiDbHandle
>dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD chetna   0
>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
>::st are not setup, RootClass ignored at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>Wed Oct 29 12:32:29 2003        INFO    Plugin
>GUS::Common::Plugin::SubmitRow registered with cvs
>revision '1.4' and cvs tag ' '
>[chetna@mkiwi chetna]$
>
>My observation is that it does work though as in
>database is updated. Just for information - is it okey
>to ignore them.
>
>Thanks
>Chetna
>
>__________________________________
>Do you Yahoo!?
>Exclusive Video Premiere - Britney Spears
>http://launch.yahoo.com/promos/britneyspears/
>  
>

[Gusdev-gusdev] Error: subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, RootClass ignored at

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

Hello All,

While I am running ga +meta --commit or ga + create

I getting this error:

[chetna@mkiwi chetna]$  ga +create
GUS::Common::Plugin::SubmitRow --commit
Reading properties from
/var/local/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/chetna/.gus.properties
GUS::ObjRelP::DbiDbHandle
dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD chetna   0
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
GUS::ObjRelP::DbiDbHandle
dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD chetna
chetna123  0 1DBI subclasses
'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
setup, RootClass ignored at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
GUS::ObjRelP::DbiDbHandle
dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD chetna   0
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
::st are not setup, RootClass ignored at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
Wed Oct 29 12:32:29 2003        INFO    Plugin
GUS::Common::Plugin::SubmitRow registered with cvs
revision '1.4' and cvs tag ' '
[chetna@mkiwi chetna]$

My observation is that it does work though as in
database is updated. Just for information - is it okey
to ignore them.

Thanks
Chetna

__________________________________
Do you Yahoo!?
Exclusive Video Premiere - Britney Spears
http://launch.yahoo.com/promos/britneyspears/

Re: [Gusdev-gusdev] DBD::Oracle::db prepare failed

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

glad to hear that, and sorry that you had difficulty.

steev

Chetna Warade wrote:

>Hello Steve,
>
>I tried locating the problem and have fixed it today morning.
>It took me a while to find out whats the problem but it seems
>that there could be two reasons (1) since the installation
>failed for me for the first time some inconsistency with the
>permissions happened to the files that were not installed
>properly Or (2) I may have missed a build step in the process
>of debugging the failed installation.
>
>Having said that my obeservation is if I start everything from
> scratch and follow the documentation it worked for me.
>
>Thanks
>Chetna
>
>---- Original message ----
>  
>
>>Date: Mon, 27 Oct 2003 18:23:15 -0500
>>From: Steve Fischer <sfi...@pc...>  
>>Subject: Re: [Gusdev-gusdev] DBD::Oracle::db prepare failed  
>>To: Chetna Warade <wa...@ya...>
>>Cc: gus...@li..., jki...@ug...
>>
>>Chetna-
>>
>>I am not sure what is causing the problem.
>>
>>However, I can see that the code which is failing is not
>>    
>>
>doing the best 
>  
>
>>job of reporting what went wrong.
>>
>>How about you make the following patch to the file 
>>$PROJECT_HOME/GUS/ObjRelP/lib/perl/DbiDbHandle.pm:
>>
>>On around line 74 you will find the method  prepareAndExecute.
>>
>>Comment it out, and replace it with this:
>>
>>sub prepareAndExecute {
>> my ($self, $sql_cmd) = @_;
>> if ($verbose) { print STDERR"\n\nprepareAndExecute:
>>    
>>
>$sql_cmd \n"; }
>  
>
>> my $sth = $self->prepare($sql_cmd) || print STDERR "Prepare
>>    
>>
>FAILED: " 
>  
>
>>. $self->errstr() . "\n sql_cmd:  \n $sql_cmd \n";
>> $sth->execute() || print STDERR "Execute FAILED: " .
>>    
>>
>$self->errstr() . 
>  
>
>>"\n sql_cmd:  \n $sql_cmd \n";
>> return $sth;
>>}
>>
>>then try the build again.
>>
>>let me know what happens.
>>
>>steve
>>
>>Chetna Warade wrote:
>>
>>    
>>
>>>Hello All,
>>>
>>>I have followed the step by step documentation from
>>>Terry and also reffered section 2.4 but I am still
>>>getting the same error:  I am also printing the values
>>>such as userid, host etc.. that assures that the login
>>>exists,
>>>Here's snapshot:
>>>
>>># build GUS install -append
>>>
>>>ant -f /var/local/checkout/install/build.xml install
>>>-Dproj=GUS -DtargetDir=/var/local/gus_home -Dcomp=
>>>-DprojectsDir=/var/local/checkout  -Dappend=true  
>>>-logger org.apache.tools.ant.NoBannerLogger | grep ']'
>>>
>>>    [echo] .
>>>    [echo] Installing CBIL/Bio
>>>    [echo] .
>>>    [echo] Installing CBIL/CSP
>>>    [echo] .
>>>    [echo] Installing CBIL/Util
>>>  [concat] Warning: Could not find any of the files
>>>specified in concat task.
>>>    [echo] .
>>>    [echo] Installing GUS/Common
>>>    [echo] .
>>>    [echo] Installing GUS/DBAdmin
>>>    [echo] .
>>>    [echo] Installing GUS/GOPredict
>>>    [echo] .
>>>    [echo] Installing GUS/ObjRelP
>>>    [echo] generating Perl Objects
>>>    [exec] Reading properties from
>>>/root/.gus.properties
>>>    [exec] DBI subclasses
>>>'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
>>>setup, RootClass ignored at
>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>>>line 152
>>>    [exec] DBD::Oracle::db prepare failed: ORA-00942:
>>>table or view does not exist (DBD ERROR:
>>>OCIStmtExecute/Describe) at
>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>>>line 78.
>>>    [exec] prepareAndExecute FAILED:
>>>GUS::ObjRelP::DbiDbHandle=HASH(0x83dd120)->errstr
>>>    [exec] Can't call method "execute" without a
>>>package or object reference at
>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>>>line 79.
>>>    [exec] GUS::ObjRelP::DbiDbHandle
>>>dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD GUSReadOnly
>>>GUSReadOnly1111  0 1
>>>
>>>BUILD FAILED
>>>file:/var/local/checkout/GUS/build.xml:194: exec
>>>returned: -1
>>>
>>>Total time: 6 seconds
>>>
>>>Thanks in advance,
>>>Chetna
>>>
>>>
>>>--- Terry Clark <tw...@cs...> wrote:
>>> 
>>>
>>>      
>>>
>>>>Chetna, this looks like the circular dependence in
>>>>the build. 
>>>>There's a work around for this documented at 
>>>> 
>>>>http://www.gusdb.org/documentation/installguide.html
>>>>in section 2.4.
>>>>
>>>>Terry
>>>>   
>>>>
>>>>        
>>>>
>>>
>>>
>>>__________________________________
>>>Do you Yahoo!?
>>>The New Yahoo! Shopping - with improved product search
>>>http://shopping.yahoo.com
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.net email is sponsored by: The SF.net Donation Program.
>>>Do you like what SourceForge.net is doing for the Open
>>>Source Community?  Make a contribution, and help us add new
>>>features and functionality. Click here:
>>>      
>>>
>http://sourceforge.net/donate/
>  
>
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> 
>>>
>>>      
>>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: The SF.net Donation Program.
>>Do you like what SourceForge.net is doing for the Open
>>Source Community?  Make a contribution, and help us add new
>>features and functionality. Click here:
>>    
>>
>http://sourceforge.net/donate/
>  
>
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>    
>>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: SF.net Giveback Program.
>Does SourceForge.net help you be more productive?  Does it
>help you create better code?   SHARE THE LOVE, and help us help
>YOU!  Click Here: http://sourceforge.net/donate/
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] DBD::Oracle::db prepare failed

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

Hello Steve,

I tried locating the problem and have fixed it today morning.
It took me a while to find out whats the problem but it seems
that there could be two reasons (1) since the installation
failed for me for the first time some inconsistency with the
permissions happened to the files that were not installed
properly Or (2) I may have missed a build step in the process
of debugging the failed installation.

Having said that my obeservation is if I start everything from
 scratch and follow the documentation it worked for me.

Thanks
Chetna

---- Original message ----
>Date: Mon, 27 Oct 2003 18:23:15 -0500
>From: Steve Fischer <sfi...@pc...>  
>Subject: Re: [Gusdev-gusdev] DBD::Oracle::db prepare failed  
>To: Chetna Warade <wa...@ya...>
>Cc: gus...@li..., jki...@ug...
>
>Chetna-
>
>I am not sure what is causing the problem.
>
>However, I can see that the code which is failing is not
doing the best 
>job of reporting what went wrong.
>
>How about you make the following patch to the file 
>$PROJECT_HOME/GUS/ObjRelP/lib/perl/DbiDbHandle.pm:
>
>On around line 74 you will find the method  prepareAndExecute.
>
>Comment it out, and replace it with this:
>
>sub prepareAndExecute {
>  my ($self, $sql_cmd) = @_;
>  if ($verbose) { print STDERR"\n\nprepareAndExecute:
$sql_cmd \n"; }
>
>  my $sth = $self->prepare($sql_cmd) || print STDERR "Prepare
FAILED: " 
>. $self->errstr() . "\n sql_cmd:  \n $sql_cmd \n";
>  $sth->execute() || print STDERR "Execute FAILED: " .
$self->errstr() . 
>"\n sql_cmd:  \n $sql_cmd \n";
>  return $sth;
>}
>
>then try the build again.
>
>let me know what happens.
>
>steve
>
>Chetna Warade wrote:
>
>>Hello All,
>>
>>I have followed the step by step documentation from
>>Terry and also reffered section 2.4 but I am still
>>getting the same error:  I am also printing the values
>>such as userid, host etc.. that assures that the login
>>exists,
>>Here's snapshot:
>>
>># build GUS install -append
>>
>>ant -f /var/local/checkout/install/build.xml install
>>-Dproj=GUS -DtargetDir=/var/local/gus_home -Dcomp=
>>-DprojectsDir=/var/local/checkout  -Dappend=true  
>>-logger org.apache.tools.ant.NoBannerLogger | grep ']'
>>
>>     [echo] .
>>     [echo] Installing CBIL/Bio
>>     [echo] .
>>     [echo] Installing CBIL/CSP
>>     [echo] .
>>     [echo] Installing CBIL/Util
>>   [concat] Warning: Could not find any of the files
>>specified in concat task.
>>     [echo] .
>>     [echo] Installing GUS/Common
>>     [echo] .
>>     [echo] Installing GUS/DBAdmin
>>     [echo] .
>>     [echo] Installing GUS/GOPredict
>>     [echo] .
>>     [echo] Installing GUS/ObjRelP
>>     [echo] generating Perl Objects
>>     [exec] Reading properties from
>>/root/.gus.properties
>>     [exec] DBI subclasses
>>'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
>>setup, RootClass ignored at
>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>>line 152
>>     [exec] DBD::Oracle::db prepare failed: ORA-00942:
>>table or view does not exist (DBD ERROR:
>>OCIStmtExecute/Describe) at
>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>>line 78.
>>     [exec] prepareAndExecute FAILED:
>>GUS::ObjRelP::DbiDbHandle=HASH(0x83dd120)->errstr
>>     [exec] Can't call method "execute" without a
>>package or object reference at
>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>>line 79.
>>     [exec] GUS::ObjRelP::DbiDbHandle
>>dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD GUSReadOnly
>>GUSReadOnly1111  0 1
>>
>>BUILD FAILED
>>file:/var/local/checkout/GUS/build.xml:194: exec
>>returned: -1
>>
>>Total time: 6 seconds
>>
>>Thanks in advance,
>>Chetna
>>
>>
>>--- Terry Clark <tw...@cs...> wrote:
>>  
>>
>>>Chetna, this looks like the circular dependence in
>>>the build. 
>>>There's a work around for this documented at 
>>>  
>>>http://www.gusdb.org/documentation/installguide.html
>>>in section 2.4.
>>>
>>>Terry
>>>    
>>>
>>
>>
>>
>>
>>__________________________________
>>Do you Yahoo!?
>>The New Yahoo! Shopping - with improved product search
>>http://shopping.yahoo.com
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: The SF.net Donation Program.
>>Do you like what SourceForge.net is doing for the Open
>>Source Community?  Make a contribution, and help us add new
>>features and functionality. Click here:
http://sourceforge.net/donate/
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>  
>>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: The SF.net Donation Program.
>Do you like what SourceForge.net is doing for the Open
>Source Community?  Make a contribution, and help us add new
>features and functionality. Click here:
http://sourceforge.net/donate/
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] DBD::Oracle::db prepare failed

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

Chetna-

I am not sure what is causing the problem.

However, I can see that the code which is failing is not doing the best 
job of reporting what went wrong.

How about you make the following patch to the file 
$PROJECT_HOME/GUS/ObjRelP/lib/perl/DbiDbHandle.pm:

On around line 74 you will find the method  prepareAndExecute.

Comment it out, and replace it with this:

sub prepareAndExecute {
  my ($self, $sql_cmd) = @_;
  if ($verbose) { print STDERR"\n\nprepareAndExecute: $sql_cmd \n"; }

  my $sth = $self->prepare($sql_cmd) || print STDERR "Prepare FAILED: " 
. $self->errstr() . "\n sql_cmd:  \n $sql_cmd \n";
  $sth->execute() || print STDERR "Execute FAILED: " . $self->errstr() . 
"\n sql_cmd:  \n $sql_cmd \n";
  return $sth;
}

then try the build again.

let me know what happens.

steve

Chetna Warade wrote:

>Hello All,
>
>I have followed the step by step documentation from
>Terry and also reffered section 2.4 but I am still
>getting the same error:  I am also printing the values
>such as userid, host etc.. that assures that the login
>exists,
>Here's snapshot:
>
># build GUS install -append
>
>ant -f /var/local/checkout/install/build.xml install
>-Dproj=GUS -DtargetDir=/var/local/gus_home -Dcomp=
>-DprojectsDir=/var/local/checkout  -Dappend=true  
>-logger org.apache.tools.ant.NoBannerLogger | grep ']'
>
>     [echo] .
>     [echo] Installing CBIL/Bio
>     [echo] .
>     [echo] Installing CBIL/CSP
>     [echo] .
>     [echo] Installing CBIL/Util
>   [concat] Warning: Could not find any of the files
>specified in concat task.
>     [echo] .
>     [echo] Installing GUS/Common
>     [echo] .
>     [echo] Installing GUS/DBAdmin
>     [echo] .
>     [echo] Installing GUS/GOPredict
>     [echo] .
>     [echo] Installing GUS/ObjRelP
>     [echo] generating Perl Objects
>     [exec] Reading properties from
>/root/.gus.properties
>     [exec] DBI subclasses
>'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
>setup, RootClass ignored at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>line 152
>     [exec] DBD::Oracle::db prepare failed: ORA-00942:
>table or view does not exist (DBD ERROR:
>OCIStmtExecute/Describe) at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>line 78.
>     [exec] prepareAndExecute FAILED:
>GUS::ObjRelP::DbiDbHandle=HASH(0x83dd120)->errstr
>     [exec] Can't call method "execute" without a
>package or object reference at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>line 79.
>     [exec] GUS::ObjRelP::DbiDbHandle
>dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD GUSReadOnly
>GUSReadOnly1111  0 1
>
>BUILD FAILED
>file:/var/local/checkout/GUS/build.xml:194: exec
>returned: -1
>
>Total time: 6 seconds
>
>Thanks in advance,
>Chetna
>
>
>--- Terry Clark <tw...@cs...> wrote:
>  
>
>>Chetna, this looks like the circular dependence in
>>the build. 
>>There's a work around for this documented at 
>>  
>>http://www.gusdb.org/documentation/installguide.html
>>in section 2.4.
>>
>>Terry
>>    
>>
>
>
>
>
>__________________________________
>Do you Yahoo!?
>The New Yahoo! Shopping - with improved product search
>http://shopping.yahoo.com
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: The SF.net Donation Program.
>Do you like what SourceForge.net is doing for the Open
>Source Community?  Make a contribution, and help us add new
>features and functionality. Click here: http://sourceforge.net/donate/
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] GUS WDK-Classic available

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

for those of you have shown interest, you can pick up the GUS Web 
Development Kit Classic from http://www.gusdb.org.

as you probably know, we aren't fully supporting it (instead focusing 
our effort on the next generation), so it is available kind of "as is".

steve

Re: [Gusdev-gusdev] missing Workflow modules

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

Dear Greg-

We have not been maintaining the prototype Workflow system.

However, as Chris mentions, we have been using a simpler, basically 
serial pipeline system successfully to manage the massive process (3 
months) of building our DoTS/AllGenes transcript index.

I have attached the dots build pipeline.  Also take a look at the 
GUS/Pipeline component.   When you see mention of the "liniac" that is 
the name of our compute cluster.  The Pipeline API includes some special 
case handling of it, which probably won't be pertinent to you.

I'd be glad to answer questions.

Steve

Chris Stoeckert wrote:

> Hi Greg,
> Those modules were developed as a prototype workflow for GUS2 and I am 
> pretty sure that they have not been updated. Instead we went with a 
> pipeline that Steve built for DoTS which is available. The pipeline as 
> it stands need to be improved or replaced with something approaching 
> the workflow functionality so that multiple interrelated pipelines can 
> be run and tracked. I will see what can be dug up on workflow and 
> would be very interested in what you have in mind for your 
> implementation.
>
> Chris
>
> On Tuesday, October 21, 2003, at 01:54  PM, Gregory Carl Kettler wrote:
>
>> Greetings all,
>> I've been working with Terry here at the University of Chicago, and we
>> were thinking it's time to start implementing a workflow in our GUS
>> installation.  However, it looks like the modules mentioned in the
>> Workflow Technical Report (LoadWorkflowFromXML, StartWorkflow, etc.) are
>> missing from the distribution.  Were these not updated for GUS 3.0?  If
>> not, where are they and what would be involved in updating them?
>>
>>     Greg
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.net email is sponsored by OSDN developer relations
>> Here's your chance to show off your extensive product knowledge
>> We want to know what you know. Tell us and you have a chance to win $100
>> http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by OSDN developer relations
> Here's your chance to show off your extensive product knowledge
> We want to know what you know. Tell us and you have a chance to win $100
> http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] DBD::Oracle::db prepare failed

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

Hello All,

I have followed the step by step documentation from
Terry and also reffered section 2.4 but I am still
getting the same error:  I am also printing the values
such as userid, host etc.. that assures that the login
exists,
Here's snapshot:

# build GUS install -append

ant -f /var/local/checkout/install/build.xml install
-Dproj=GUS -DtargetDir=/var/local/gus_home -Dcomp=
-DprojectsDir=/var/local/checkout  -Dappend=true  
-logger org.apache.tools.ant.NoBannerLogger | grep ']'

     [echo] .
     [echo] Installing CBIL/Bio
     [echo] .
     [echo] Installing CBIL/CSP
     [echo] .
     [echo] Installing CBIL/Util
   [concat] Warning: Could not find any of the files
specified in concat task.
     [echo] .
     [echo] Installing GUS/Common
     [echo] .
     [echo] Installing GUS/DBAdmin
     [echo] .
     [echo] Installing GUS/GOPredict
     [echo] .
     [echo] Installing GUS/ObjRelP
     [echo] generating Perl Objects
     [exec] Reading properties from
/root/.gus.properties
     [exec] DBI subclasses
'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
setup, RootClass ignored at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
     [exec] DBD::Oracle::db prepare failed: ORA-00942:
table or view does not exist (DBD ERROR:
OCIStmtExecute/Describe) at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 78.
     [exec] prepareAndExecute FAILED:
GUS::ObjRelP::DbiDbHandle=HASH(0x83dd120)->errstr
     [exec] Can't call method "execute" without a
package or object reference at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 79.
     [exec] GUS::ObjRelP::DbiDbHandle
dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD GUSReadOnly
GUSReadOnly1111  0 1

BUILD FAILED
file:/var/local/checkout/GUS/build.xml:194: exec
returned: -1

Total time: 6 seconds

Thanks in advance,
Chetna


--- Terry Clark <tw...@cs...> wrote:
> Chetna, this looks like the circular dependence in
> the build. 
> There's a work around for this documented at 
>   
> http://www.gusdb.org/documentation/installguide.html
> in section 2.4.
> 
> Terry




__________________________________
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search
http://shopping.yahoo.com

Re: [Gusdev-gusdev] registering ga: insufficient privileges

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

the only idea i have is to check your .gus.properties file to see what 
login it is using, then to do the sqlplus with that login

steve

Fidel Salas wrote:

>I am trying to register ga but have run into the following block.
>When I run "ga +meta --commit" I get a DBD::Oracle::db prepare failed
>(see below) due to apparently insufficient privileges when running the
>statement "select Core.Algorithm_SQ.NEXTVAL from DUAL."  However,
>as, also shown below, gus or core can run that command without any
>problems within sqlplus.
>
>Any ideas what might be the problem?
>
>Thanks
>
>Fidel
>
>
>
>$ ga +meta --commit
>Reading properties from /home/apps/gus/gushome/config/GUS-PluginMgr.prop
>Reading properties from /home/apps/gus/.gus.properties
>  <Core::Algorithm>
>    <name>GA-Plugin</name>
>    <description>GUS application framework for plugins</description>
>    <Core::AlgorithmImplementation>
>      <cvs_revision>1.46</cvs_revision>
>      <cvs_tag> </cvs_tag>
>      <executable>GUS::PluginMgr::GusApplication</executable>
>      <executable_md5>ca16dad3cc217300275685a02730affc</executable_md5>
>      <description>update for GUS 3.0</description>
>      <Core::AlgorithmInvocation>
>        <start_time>SYSDATE</start_time>
>        <end_time>SYSDATE</end_time>
>        <machine_id>0</machine_id>
>        <cpus_used>1</cpus_used>
>        <result>meta</result>
>      </Core::AlgorithmInvocation>
>    </Core::AlgorithmImplementation>
>  </Core::Algorithm>
>DBD::Oracle::db prepare failed: ORA-01031: insufficient privileges (DBD ERROR: OCIStmtExecute/Describe)
>[for Statement "select Core.Algorithm_SQ.NEXTVAL from DUAL"] at /home/apps/gus/gushome/lib/perl/GUS/ObjRelP/DbiTable.pm line 671.
>Can't call method "execute" on an undefined value at /home/apps/gus/gushome/lib/perl/GUS/ObjRelP/DbiTable.pm line 673.
>
>gus@tyler-lab:/home/apps/gus$ sqlplus core/xxxxxxx@guspd
>
>SQL*Plus: Release 9.2.0.1.0 - Production on Thu Oct 23 16:46:51 2003
>
>Copyright (c) 1982, 2002, Oracle Corporation.  All rights reserved.
>
>
>Connected to:
>Oracle9i Enterprise Edition Release 9.2.0.3.0 - 64bit Production
>With the Partitioning, OLAP and Oracle Data Mining options
>JServer Release 9.2.0.3.0 - Production
>
>SQL> select Core.Algorithm_SQ.NEXTVAL from DUAL;
>
>   NEXTVAL
>----------
>        21
>
>SQL> exit
>Disconnected from Oracle9i Enterprise Edition Release 9.2.0.3.0 - 64bit Production
>With the Partitioning, OLAP and Oracle Data Mining options
>JServer Release 9.2.0.3.0 - Production
>gus@tyler-lab:/home/apps/gus$ sqlplus gus/xxxxxxx@guspd
>
>SQL*Plus: Release 9.2.0.1.0 - Production on Thu Oct 23 16:47:39 2003
>
>Copyright (c) 1982, 2002, Oracle Corporation.  All rights reserved.
>
>
>Connected to:
>Oracle9i Enterprise Edition Release 9.2.0.3.0 - 64bit Production
>With the Partitioning, OLAP and Oracle Data Mining options
>JServer Release 9.2.0.3.0 - Production
>
>SQL> select Core.Algorithm_SQ.NEXTVAL from DUAL;
>
>   NEXTVAL
>----------
>        22
>
>gus@tyler-lab:/home/apps/gus$ cat .gus.properties
>databaseLogin=GUSrw
>databasePassword=xxxxxxx
>readOnlyDatabaseLogin=GUSdevReadOnly
>readOnlyDatabasePassword=xxxxxxx
>coreSchemaName=Core
>userName=gus
>group=dba
>project=Database Administration
>dbiDsn=dbi:Oracle:host=tuor;sid=guspd
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: The SF.net Donation Program.
>Do you like what SourceForge.net is doing for the Open
>Source Community?  Make a contribution, and help us add new
>features and functionality. Click here: http://sourceforge.net/donate/
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] registering ga: insufficient privileges

[Fidel S. <fi...@vb...>]

I am trying to register ga but have run into the following block.
When I run "ga +meta --commit" I get a DBD::Oracle::db prepare failed
(see below) due to apparently insufficient privileges when running the
statement "select Core.Algorithm_SQ.NEXTVAL from DUAL."  However,
as, also shown below, gus or core can run that command without any
problems within sqlplus.

Any ideas what might be the problem?

Thanks

Fidel



$ ga +meta --commit
Reading properties from /home/apps/gus/gushome/config/GUS-PluginMgr.prop
Reading properties from /home/apps/gus/.gus.properties
  <Core::Algorithm>
    <name>GA-Plugin</name>
    <description>GUS application framework for plugins</description>
    <Core::AlgorithmImplementation>
      <cvs_revision>1.46</cvs_revision>
      <cvs_tag> </cvs_tag>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <executable_md5>ca16dad3cc217300275685a02730affc</executable_md5>
      <description>update for GUS 3.0</description>
      <Core::AlgorithmInvocation>
        <start_time>SYSDATE</start_time>
        <end_time>SYSDATE</end_time>
        <machine_id>0</machine_id>
        <cpus_used>1</cpus_used>
        <result>meta</result>
      </Core::AlgorithmInvocation>
    </Core::AlgorithmImplementation>
  </Core::Algorithm>
DBD::Oracle::db prepare failed: ORA-01031: insufficient privileges (DBD ERROR: OCIStmtExecute/Describe)
[for Statement "select Core.Algorithm_SQ.NEXTVAL from DUAL"] at /home/apps/gus/gushome/lib/perl/GUS/ObjRelP/DbiTable.pm line 671.
Can't call method "execute" on an undefined value at /home/apps/gus/gushome/lib/perl/GUS/ObjRelP/DbiTable.pm line 673.

gus@tyler-lab:/home/apps/gus$ sqlplus core/xxxxxxx@guspd

SQL*Plus: Release 9.2.0.1.0 - Production on Thu Oct 23 16:46:51 2003

Copyright (c) 1982, 2002, Oracle Corporation.  All rights reserved.


Connected to:
Oracle9i Enterprise Edition Release 9.2.0.3.0 - 64bit Production
With the Partitioning, OLAP and Oracle Data Mining options
JServer Release 9.2.0.3.0 - Production

SQL> select Core.Algorithm_SQ.NEXTVAL from DUAL;

   NEXTVAL
----------
        21

SQL> exit
Disconnected from Oracle9i Enterprise Edition Release 9.2.0.3.0 - 64bit Production
With the Partitioning, OLAP and Oracle Data Mining options
JServer Release 9.2.0.3.0 - Production
gus@tyler-lab:/home/apps/gus$ sqlplus gus/xxxxxxx@guspd

SQL*Plus: Release 9.2.0.1.0 - Production on Thu Oct 23 16:47:39 2003

Copyright (c) 1982, 2002, Oracle Corporation.  All rights reserved.


Connected to:
Oracle9i Enterprise Edition Release 9.2.0.3.0 - 64bit Production
With the Partitioning, OLAP and Oracle Data Mining options
JServer Release 9.2.0.3.0 - Production

SQL> select Core.Algorithm_SQ.NEXTVAL from DUAL;

   NEXTVAL
----------
        22

gus@tyler-lab:/home/apps/gus$ cat .gus.properties
databaseLogin=GUSrw
databasePassword=xxxxxxx
readOnlyDatabaseLogin=GUSdevReadOnly
readOnlyDatabasePassword=xxxxxxx
coreSchemaName=Core
userName=gus
group=dba
project=Database Administration
dbiDsn=dbi:Oracle:host=tuor;sid=guspd

Re: [Gusdev-gusdev] missing Workflow modules

[Chris S. <sto...@pc...>]

Hi Greg,
Those modules were developed as a prototype workflow for GUS2 and I am 
pretty sure that they have not been updated. Instead we went with a 
pipeline that Steve built for DoTS which is available. The pipeline as 
it stands need to be improved or replaced with something approaching 
the workflow functionality so that multiple interrelated pipelines can 
be run and tracked. I will see what can be dug up on workflow and would 
be very interested in what you have in mind for your implementation.

Chris

On Tuesday, October 21, 2003, at 01:54  PM, Gregory Carl Kettler wrote:

> Greetings all,
> I've been working with Terry here at the University of Chicago, and we
> were thinking it's time to start implementing a workflow in our GUS
> installation.  However, it looks like the modules mentioned in the
> Workflow Technical Report (LoadWorkflowFromXML, StartWorkflow, etc.) 
> are
> missing from the distribution.  Were these not updated for GUS 3.0?  If
> not, where are they and what would be involved in updating them?
>
> 	Greg
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by OSDN developer relations
> Here's your chance to show off your extensive product knowledge
> We want to know what you know. Tell us and you have a chance to win 
> $100
> http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] DBD::Oracle::db prepare failed

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

Chetna, this looks like the circular dependence in the build. 
There's a work around for this documented at 
   http://www.gusdb.org/documentation/installguide.html
in section 2.4.

Terry


On  0, Chetna Warade <wa...@ya...> wrote:
> We are trying to install GUS 3.0 from scratch and
> following almost all documentations.
> 
> We are little confused here for the following reasons:
> 
> The GUS documentation says to do:
> Initial build system - (this is failing for us) that
> generates schema creation scritps. Then execute  the
> create-db.sh.
> 
> The error below is about "table or view not found" Are
> there any tables/views besides the 5 known
> (core,rad3,sres,tess,dots) schemas?
> 
> 
> 
> [root@mkiwi install]# build GUS install -append
> 
> ant -f /var/local/checkout/install/build.xml install
> -Dproj=GUS -DtargetDir=/var/local/gus_home -Dcomp=
> -DprojectsDir=/var/local/checkout  -Dappend=true  
> -logger org.apache.tools.ant.NoBannerLogger | grep ']'
> 
>      [echo] .
>      [echo] Installing CBIL/Bio
>      [echo] .
>      [echo] Installing CBIL/CSP
>      [echo] .
>      [echo] Installing CBIL/Util
>    [concat] Warning: Could not find any of the files
> specified in concat task.
>      [echo] .
>      [echo] Installing GUS/Common
>      [echo] .
>      [echo] Installing GUS/DBAdmin
>      [echo] .
>      [echo] Installing GUS/GOPredict
>      [echo] .
>      [echo] Installing GUS/ObjRelP
>      [echo] generating Perl Objects
>      [exec] Reading properties from
> /root/.gus.properties
>      [exec] DBI subclasses
> 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
> setup, RootClass ignored at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 152
>      [exec] DBD::Oracle::db prepare failed: ORA-00942:
> table or view does not exist (DBD ERROR:
> OCIStmtExecute/Describe) at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 78.
>      [exec] prepareAndExecute FAILED:
> GUS::ObjRelP::DbiDbHandle=HASH(0x83dd120)->errstr
>      [exec] Can't call method "execute" without a
> package or object reference at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 79.
>      [exec] GUS::ObjRelP::DbiDbHandle
> dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD GUSReadOnly
> GUSReadOnly1111  0 1
> 
> BUILD FAILED
> file:/var/local/checkout/GUS/build.xml:194: exec
> returned: -1
> 
> Total time: 6 seconds
> [root@mkiwi install]#
> 
> Thanks,
> Chetna
> 
> 
> 
> __________________________________
> Do you Yahoo!?
> The New Yahoo! Shopping - with improved product search
> http://shopping.yahoo.com
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by OSDN developer relations
> Here's your chance to show off your extensive product knowledge
> We want to know what you know. Tell us and you have a chance to win $100
> http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] DBD::Oracle::db prepare failed

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

We are trying to install GUS 3.0 from scratch and
following almost all documentations.

We are little confused here for the following reasons:

The GUS documentation says to do:
Initial build system - (this is failing for us) that
generates schema creation scritps. Then execute  the
create-db.sh.

The error below is about "table or view not found" Are
there any tables/views besides the 5 known
(core,rad3,sres,tess,dots) schemas?



[root@mkiwi install]# build GUS install -append

ant -f /var/local/checkout/install/build.xml install
-Dproj=GUS -DtargetDir=/var/local/gus_home -Dcomp=
-DprojectsDir=/var/local/checkout  -Dappend=true  
-logger org.apache.tools.ant.NoBannerLogger | grep ']'

     [echo] .
     [echo] Installing CBIL/Bio
     [echo] .
     [echo] Installing CBIL/CSP
     [echo] .
     [echo] Installing CBIL/Util
   [concat] Warning: Could not find any of the files
specified in concat task.
     [echo] .
     [echo] Installing GUS/Common
     [echo] .
     [echo] Installing GUS/DBAdmin
     [echo] .
     [echo] Installing GUS/GOPredict
     [echo] .
     [echo] Installing GUS/ObjRelP
     [echo] generating Perl Objects
     [exec] Reading properties from
/root/.gus.properties
     [exec] DBI subclasses
'GUS::ObjRelP::DbiDbHandle::db' and ::st are not
setup, RootClass ignored at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
line 152
     [exec] DBD::Oracle::db prepare failed: ORA-00942:
table or view does not exist (DBD ERROR:
OCIStmtExecute/Describe) at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 78.
     [exec] prepareAndExecute FAILED:
GUS::ObjRelP::DbiDbHandle=HASH(0x83dd120)->errstr
     [exec] Can't call method "execute" without a
package or object reference at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 79.
     [exec] GUS::ObjRelP::DbiDbHandle
dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD GUSReadOnly
GUSReadOnly1111  0 1

BUILD FAILED
file:/var/local/checkout/GUS/build.xml:194: exec
returned: -1

Total time: 6 seconds
[root@mkiwi install]#

Thanks,
Chetna



__________________________________
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search
http://shopping.yahoo.com

[Gusdev-gusdev] missing Workflow modules

[Gregory C. K. <gck...@cs...>]

Greetings all,
I've been working with Terry here at the University of Chicago, and we
were thinking it's time to start implementing a workflow in our GUS
installation.  However, it looks like the modules mentioned in the
Workflow Technical Report (LoadWorkflowFromXML, StartWorkflow, etc.) are
missing from the distribution.  Were these not updated for GUS 3.0?  If
not, where are they and what would be involved in updating them?

	Greg

Re: [Gusdev-gusdev] ga problem

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

Steve-

On Mon, 6 Oct 2003, Steve Fischer wrote:
> which workaround?  the original one you put in place is this, at the end 
> of DbiDbHandle.pm:
> 
> 
> # JC 9/6/2002
> #
> # Subclassing not set up correctly according to DBI manpage;
> # this appears to fix it, although the structure is still
> # a little off.  The fact that we're reblessing the return
> # value from the DBI connect() method is making everything
> # work, albeit in a roundabout way.
> #
> package GUS::ObjRelP::DbiDbHandle::db;
> use vars qw(@ISA);
> @ISA = qw( DBI::db );
> 
> Thats been in place for ages.
> 
> is there another one?  
> 

Yes; for more recent versions of DBI and/or Perl (I forget the exact 
details) I also added the following lines--

package DbiDbHandle::st;
use vars qw(@ISA);
@ISA = qw( DBI::st );

Locally e2kroos has this patch (installed in 
/usr/lib/perl5/site_perl/5.6.1/Objects/dbiperl_utils) and I thought I'd 
mentioned it in an e-mail earlier, but perhaps not.

Jonathan

Re: [Gusdev-gusdev] how to install GUS graphic interface?

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

Dear Sam-

We are starting a project now to develop the next generation of the GUS 
Web Development Kit (WDK) which will use JSP and Struts.  We plan to 
support and distribute that as part of GUS.

In the meantime, we are using the GUS WDK "Classic" which uses Java 
Servlets.  We do not plan on supporting the WDK Classic.  However, we 
are preparing to make the code available and to provide some minimal 
documentation.  Other groups (such as the PSU at Sanger and Jessie's 
group at UGA have made good use of the WDK Classic.  I hope to have it 
posted by the end of next week.

steve


sam wang wrote:

> Dear friends,
>  
> does gus have graphic user interface to work with? for example, 
> uploading or querying data? if the interface use Jsp/Servlet 
> technology or Perl CGI? if Jsp/Servlet, I guess there need install 
> Apache or Tomcat in order to use the GUI, or sometime maybe Tomcat 
> alone is enough. I don't know which technology GUS  take. does there 
> any guide about how to install and configure the GUI of GUS? since I 
> have installed GUS successfully, I am very eager to work with it! but 
> the problem is that I don't know how can I use it :-(
>  
> thank you very much for your help in advance!
> Sammy
> ------------------------------------------------------------------------
> Do you Yahoo!?
> The New Yahoo! Shopping 
> <http://shopping.yahoo.com/?__yltc=s%3A150000443%2Cd%3A22708228%2Cslk%3Atext%2Csec%3Amail> 
> - with improved product search 

[Gusdev-gusdev] how to install GUS graphic interface?

[sam w. <gus...@ya...>]

Dear friends,
 
does gus have graphic user interface to work with? for example, uploading or querying data? if the interface use Jsp/Servlet technology or Perl CGI? if Jsp/Servlet, I guess there need install Apache or Tomcat in order to use the GUI, or sometime maybe Tomcat alone is enough. I don't know which technology GUS  take. does there any guide about how to install and configure the GUI of GUS? since I have installed GUS successfully, I am very eager to work with it! but the problem is that I don't know how can I use it :-(
 
thank you very much for your help in advance!
Sammy


---------------------------------
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search

Re: [Gusdev-gusdev] missing GO modules

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

Hey Terry, sorry for not getting back sooner on this.

The classes have all been merged into one table, 'GOAssociation,' which 
makes associations between a generic row in the database (usually 
representing a sequence, and indicated by the 'table_id' and 'row_id' 
attributes in the GOAssociation table) and a GO Term.

I'm not sure what the plugin uses those tables for, let me take a look and 
make sure it's nothing out of the ordinary.  Generally, converting to GUS 
3.0 is a matter of simply understanding the schema and a few of the new 
conventions that plugins follow.  I will send you a document (if for 
nothing else than posterity) that has general details about the process.

Dave

On Wed, 1 Oct 2003, Terry Clark wrote:

> I just stumbled into some modules missing in
> the current GUS distribution that are 
> used by plugin LoadGeneFeaturesFromXML.pm :
> 
>   require GUS::Model::DoTS::AASequenceGOProcess;
>   require GUS::Model::DoTS::AASequenceGOComponent;
>   require GUS::Model::DoTS::AASequenceGOFunction;
> 
>   require GUS::Model::DoTS::ProteinGOProcess;
>   require GUS::Model::DoTS::ProteinGOComponent;
>   require GUS::Model::DoTS::ProteinGOFunction;
> 
> It looks like they have not been converted to GUS 3.0 yet
> (with a strong hint in TASK_GoAnnotation(): ### NOTE: NOT YET UPDATED).
> I'm willing to take a shot at updating these, but I don't
> know where to find them (and what's involved in converting 
> 2.0 to 3.0 so I should be careful about volunteering ;-)
> 
> Terry
> 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

[Gusdev-gusdev] oracle database relocation error!

[sam w. <gus...@ya...>]

Dear friends,

 

after I install GUS project successfully, I found there is a problem, sometime the oracle database will crash when I operate in oemapp console. there is no any response of the database. after checking log file, I found there are many relocation error about a lib of oracle. I don't know what's the reason of this problem? I used oracle dataware house type, not general type. or if this problem relate to GUS installation or the worst case, there is some problem when I install oracle on linux? I know it's a specific problem and maybe not relate to GUS project. if you happen to know the reason, please let me know. or if you need detail description of this problem, please let me know.

 

thank you very much and best wishes!

 

Sammy



---------------------------------
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search

Re: [Gusdev-gusdev] ga problem

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

jonathan-

which workaround?  the original one you put in place is this, at the end 
of DbiDbHandle.pm:


# JC 9/6/2002
#
# Subclassing not set up correctly according to DBI manpage;
# this appears to fix it, although the structure is still
# a little off.  The fact that we're reblessing the return
# value from the DBI connect() method is making everything
# work, albeit in a roundabout way.
#
package GUS::ObjRelP::DbiDbHandle::db;
use vars qw(@ISA);
@ISA = qw( DBI::db );

Thats been in place for ages.

is there another one?  

i think that there may be something else going on here, having to do 
with version of perl,  or something.

steve

Jonathan Crabtree wrote:

>Hi Sam-
>
>On Sat, 4 Oct 2003, sam wang wrote:
>  
>
>>DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, 
>>RootClass ignored at 
>>    
>>
>
>The above error is annoying, but should not affect the correct operation 
>of the plugin.  It has to do with the way that the DBI classes are subclassed 
>in the GUS code, and a workaround is available (could someone commit this 
>to CVS?)
>
>  
>
>>DBD::Oracle::st execute failed: ORA-02291: integrity constraint 
>>(CORE.ALGORITHMINVOCATION_FK04) violated - parent key not found (DBD ERROR: 
>>OCIStmtExecute) [for statement ``
>>    INSERT INTO Core.AlgorithmInvocation (  group_read, user_read, 
>>algorithm_implementation_id, modification_date, end_time,
>>other_write, row_group_id, machine_id, user_write, other_read, 
>>group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, 
>>row_project_id, algorithm_invocation_id, result )
>>    VALUES   (  ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, 
>>SYSDATE, ?, ?, ?, ?, ? ) '' with params: :p5='1', :p12=1, :p8=1, :p14='2', 
>>:p10=1, :p13='1', :p2=1, :p6=0, :p3='2', :p15='meta', :p7=1, :p1=1, :p4=0, 
>>:p9=1, :p11='1']) at 
>>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
>> 
>> SQL ERROR!! involving
>>  
>>    INSERT INTO Core.AlgorithmInvocation (  group_read, user_read, 
>>algorithm_implementation_id, modification_date, end_time,
>>other_write, row_group_id, machine_id, user_write, other_read, 
>>group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, 
>>row_project_id, algorithm_invocation_id, result )
>>    VALUES   (  ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, 
>>SYSDATE, ?, ?, ?, ?, ? )
>> Values: 1, 1, 2, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 2, meta at 
>>/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
>>    
>>
>
>Now this is the real error; a failed INSERT statement.  Notice that the 
>error mentions a violation of the integrity constraint 
>"CORE.ALGORITHMINVOCATION_FK04".  You can find the definition of this 
>constraint in the file GUS/Model/schema/oracle/core-constraints.sql (from 
>the GUS CVS repository):
>
>alter table @oracle_core@.ALGORITHMINVOCATION add constraint 
>ALGORITHMINVOCATION_FK04 foreign key (MACHINE_ID) references 
>@oracle_core@.MACHINE (MACHINE_ID);
>
>So the problem is that your INSERT statement is referencing a nonexistent 
>row in core.Machine (namely the one with machine_id = 0).  Insert this 
>missing row into the core.Machine table (using SQL*PLUS, since you won't 
>be able to do it with 'ga' until the problem is fixed) and it should 
>allow the insert to succeed.
>
>Jonathan
>
>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] ga problem

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

Hi Sam-

On Sat, 4 Oct 2003, sam wang wrote:
> DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, 
> RootClass ignored at 

The above error is annoying, but should not affect the correct operation 
of the plugin.  It has to do with the way that the DBI classes are subclassed 
in the GUS code, and a workaround is available (could someone commit this 
to CVS?)

> DBD::Oracle::st execute failed: ORA-02291: integrity constraint 
> (CORE.ALGORITHMINVOCATION_FK04) violated - parent key not found (DBD ERROR: 
> OCIStmtExecute) [for statement ``
>     INSERT INTO Core.AlgorithmInvocation (  group_read, user_read, 
> algorithm_implementation_id, modification_date, end_time,
> other_write, row_group_id, machine_id, user_write, other_read, 
> group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, 
> row_project_id, algorithm_invocation_id, result )
>     VALUES   (  ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, 
> SYSDATE, ?, ?, ?, ?, ? ) '' with params: :p5='1', :p12=1, :p8=1, :p14='2', 
> :p10=1, :p13='1', :p2=1, :p6=0, :p3='2', :p15='meta', :p7=1, :p1=1, :p4=0, 
> :p9=1, :p11='1']) at 
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
>  
>  SQL ERROR!! involving
>   
>     INSERT INTO Core.AlgorithmInvocation (  group_read, user_read, 
> algorithm_implementation_id, modification_date, end_time,
> other_write, row_group_id, machine_id, user_write, other_read, 
> group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, 
> row_project_id, algorithm_invocation_id, result )
>     VALUES   (  ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, 
> SYSDATE, ?, ?, ?, ?, ? )
>  Values: 1, 1, 2, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 2, meta at 
> /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

Now this is the real error; a failed INSERT statement.  Notice that the 
error mentions a violation of the integrity constraint 
"CORE.ALGORITHMINVOCATION_FK04".  You can find the definition of this 
constraint in the file GUS/Model/schema/oracle/core-constraints.sql (from 
the GUS CVS repository):

alter table @oracle_core@.ALGORITHMINVOCATION add constraint 
ALGORITHMINVOCATION_FK04 foreign key (MACHINE_ID) references 
@oracle_core@.MACHINE (MACHINE_ID);

So the problem is that your INSERT statement is referencing a nonexistent 
row in core.Machine (namely the one with machine_id = 0).  Insert this 
missing row into the core.Machine table (using SQL*PLUS, since you won't 
be able to do it with 'ga' until the problem is fixed) and it should 
allow the insert to succeed.

Jonathan

[Gusdev-gusdev] ga problem

[sam w. <gus...@ya...>]

Dear friends,
 
at last I got the following result when I try to install GUS project:
     ......
     [copy] Copying 2 files to /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS
     [echo] Starting target: JavaModel
     [echo] .
     [echo] Installing GUS/Model
     [copy] Copying 1291 files to /home/gus/run/lib/perl/GUS/Model
     [echo] .
     [echo] Installing GUS/Pipeline
     [echo] .
     [echo] Installing GUS/PluginMgr
     [echo] .
     [echo] Installing GUS/SchemaBrowser
   [concat] Warning: Could not find any of the files specified in concat task.

This was the same way the installation on kaveri ended, and so I guess the installation on my machine a success.
 
but then when I want to register ga using the command: ga +meta --commit
I got the following result, please see the bottom of this email in details.
 
so I don't know how to fix this problem, any hint will be great appreciate. besides, sorry for the long line below.
 
best wishes!
Sammy
 
 
the following is the result of command: ga +meta --commit
 
 
[oracle@GUS bin]$ ga +meta --commit
Reading properties from /opt/gus/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/oracle/.gus.properties
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, 
RootClass ignored at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, 
RootClass ignored at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 152
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup, 
RootClass ignored at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 152
  <Core::Algorithm>
    <name>GA-Plugin</name>
    <description>GUS application framework for plugins</description>
    <Core::AlgorithmImplementation>
      <cvs_revision>1.46</cvs_revision>
      <cvs_tag> </cvs_tag>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <executable_md5>ca16dad3cc217300275685a02730affc</executable_md5>
      <description>update for GUS 3.0</description>
      <Core::AlgorithmInvocation>
        <start_time>SYSDATE</start_time>
        <end_time>SYSDATE</end_time>
        <machine_id>0</machine_id>
        <cpus_used>1</cpus_used>
        <result>meta</result>
      </Core::AlgorithmInvocation>
    </Core::AlgorithmImplementation>
  </Core::Algorithm>
DBD::Oracle::st execute failed: ORA-02291: integrity constraint 
(CORE.ALGORITHMINVOCATION_FK04) violated - parent key not found (DBD ERROR: 
OCIStmtExecute) [for statement ``
    INSERT INTO Core.AlgorithmInvocation (  group_read, user_read, 
algorithm_implementation_id, modification_date, end_time,
other_write, row_group_id, machine_id, user_write, other_read, 
group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, 
row_project_id, algorithm_invocation_id, result )
    VALUES   (  ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, 
SYSDATE, ?, ?, ?, ?, ? ) '' with params: :p5='1', :p12=1, :p8=1, :p14='2', 
:p10=1, :p13='1', :p2=1, :p6=0, :p3='2', :p15='meta', :p7=1, :p1=1, :p4=0, 
:p9=1, :p11='1']) at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
 
 SQL ERROR!! involving
  
    INSERT INTO Core.AlgorithmInvocation (  group_read, user_read, 
algorithm_implementation_id, modification_date, end_time,
other_write, row_group_id, machine_id, user_write, other_read, 
group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, 
row_project_id, algorithm_invocation_id, result )
    VALUES   (  ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, 
SYSDATE, ?, ?, ?, ?, ? )
 Values: 1, 1, 2, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 2, meta at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
        
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x864bb04)','\x{a} SQL ERROR!! involving\x{a} \x{a}
   INSERT INTO Core.AlgorithmInvoc...') called at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
        
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x864bb04)','DBI::st=HASH(0x879dde8)','ARRAY(0x879ddb8)','\x{a}    
INSERT INTO Core.AlgorithmInvocation (  group_read, user...') called at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
        
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86fb340)','HASH(0x879ee88)') called at 
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621
        
GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86fb340)') called at 
/opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
        
GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86fb340)','undef',1) called at 
/opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
        
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmImplementation=HASH(0x86c3634)','GUS::Model::Core::AlgorithmInvocation') 
called at /opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
        
GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplementation=HASH(0x86c3634)') called at 
/opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
        
GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x86c3634)','undef',1) called at 
/opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
        
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x864ba08)','GUS::Model::Core::AlgorithmImplementation') 
called at /opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
        
GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x864ba08)') called at 
/opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
        
GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x864ba08)') called at 
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 355
        
GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','undef') called at
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
        
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','undef') called at 
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
        
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060680)') called at 
/opt/gus/gus_home/bin/ga line 11



---------------------------------
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search

Re: [Gusdev-gusdev] Boolean query error

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

Hi

I think we found a way to fix this problem.

We've added
this line
    => stmt.setQueryTimeout (this.maxQueryTimeout);
in the getStatement() method in ConnectionPool class.

As a consequence the inner class Reaper in ConnectionPool is not in use
any longer.

cheers
Arnaud

public Statement getStatement() {

    / / ...

    stmt.setQueryTimeout (this.maxQueryTimeout);

    // ...

} catch (SQLException sqle) {
    // ...
}

Steve Fischer wrote:

> ok.  then just to clarify a dead horse, the Boolean query error is a
> secondary effect.  the primary problem, as i think you guys have been
> exploring, is that we are not handling timed out queries correctly.
> in particular, as arnaud speculates, we are getting an entry in
> Queries which points to a non-existent cache table.
>
> steve
>
> Arnaud Kerhornou wrote:
>
>> That's all correct.
>>
>> I haven't investigated further but I reckon the reference to the
>> non-existent
>> cache table in an entry in the queries table (correct me if I'm
>> wrong). So we
>> need a way to delete this entry or roll it back if it is possible.
>>
>> Quoting Steve Fischer <st...@pc...>:
>>
>>
>> > if i understand paul correctly, then the problem is this:
>> >   1. query 1 produces SQLIdResultTable_1
>> >   2. query 2 times out, leaving as an artifact a broken
>> > SQLIdResultTable, ie one without a valid cached result.
>> >   3. the boolean intersect operator tries to intersect these and
>> > bombs
>> > out, producing an empty result?
>> >   4. is it also the case that if the user tries to redo query 2,
>> > outside
>> > of the boolean context, then it again produces no result because it
>> > is
>> > trying to reference the non-existent cache table?
>> >
>> > steve
>> >
>> >
>> > Pjm wrote:
>> >
>> >
>> >>  Adrian Roy Tivey wrote:
>> >>
>> >>
>> >> >>  Arnaud-
>> >> >>
>> >> >>  Jonathan has handed responsibility for the WDK over to me and
>> >> >>  Angel,
>> >> >>  since he has moved to D.C.
>> >> >>
>> >> >>  I'll look into it.  Feel free to delve into the code and find
>> >> >>  out
>> >> >>  whatever you can.
>> >> >>
>> >> >>  Steve
>> >> >>
>> >> > Does anybody know how reliable Statement.setQueryTimeout is on
>> >> > Oracle? If it's
>> >> > robust we could easily switch to that. Then we get the timeout
>> >> > report
>> >> > in (more
>> >> > or less) the right bit of the code to handle it.
>> >> >
>> >>  The statement timeout code works fine. Its more the fact that if
>> >>  one
>> >>  of the sub queries fails (for whatever reason) then the
>> >>  cacheXXXX
>> >>  table does not get created. Thus the query that intersects with
>> >>  it
>> >>  will also fail. The code does not handle this and the results
>> >>  page has
>> >>  a table with no rows.
>> >>
>> >>  The next time that query runs it will look for the cacheXXXX
>> >>  table and
>> >>  fail. The user will think the query found nothing.
>> >>
>> >>  Paul.
>> >>
>> >>

Re: [Gusdev-gusdev] Boolean query error

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

ok.  then just to clarify a dead horse, the Boolean query error is a 
secondary effect.  the primary problem, as i think you guys have been 
exploring, is that we are not handling timed out queries correctly.  in 
particular, as arnaud speculates, we are getting an entry in Queries 
which points to a non-existent cache table.

steve

Arnaud Kerhornou wrote:

>That's all correct.
>
>I haven't investigated further but I reckon the reference to the non-existent
>cache table in an entry in the queries table (correct me if I'm wrong). So we
>need a way to delete this entry or roll it back if it is possible.
>
>Quoting Steve Fischer <st...@pc...>:
>
>  
>
>>if i understand paul correctly, then the problem is this:
>>  1. query 1 produces SQLIdResultTable_1
>>  2. query 2 times out, leaving as an artifact a broken 
>>SQLIdResultTable, ie one without a valid cached result.
>>  3. the boolean intersect operator tries to intersect these and bombs 
>>out, producing an empty result?
>>  4. is it also the case that if the user tries to redo query 2, outside 
>>of the boolean context, then it again produces no result because it is 
>>trying to reference the non-existent cache table?
>>
>>steve
>>
>>
>>Pjm wrote:
>>
>>    
>>
>>>Adrian Roy Tivey wrote:
>>>
>>>      
>>>
>>>>>Arnaud-
>>>>>
>>>>>Jonathan has handed responsibility for the WDK over to me and Angel, 
>>>>>since he has moved to D.C.
>>>>>
>>>>>I'll look into it.  Feel free to delve into the code and find out 
>>>>>whatever you can.
>>>>>
>>>>>Steve
>>>>>          
>>>>>
>>>>
>>>>Does anybody know how reliable Statement.setQueryTimeout is on 
>>>>Oracle? If it's
>>>>robust we could easily switch to that. Then we get the timeout report 
>>>>in (more
>>>>or less) the right bit of the code to handle it.
>>>>        
>>>>
>>>The statement timeout code works fine. Its more the fact that if one 
>>>of the sub queries fails (for whatever reason) then the cacheXXXX 
>>>table does not get created. Thus the query that intersects with it 
>>>will also fail. The code does not handle this and the results page has 
>>>a table with no rows.
>>>
>>>The next time that query runs it will look for the cacheXXXX table and 
>>>fail. The user will think the query found nothing.
>>>
>>>Paul.
>>>
>>>      
>>>
>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] missing GO modules

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

I just stumbled into some modules missing in
the current GUS distribution that are 
used by plugin LoadGeneFeaturesFromXML.pm :

  require GUS::Model::DoTS::AASequenceGOProcess;
  require GUS::Model::DoTS::AASequenceGOComponent;
  require GUS::Model::DoTS::AASequenceGOFunction;

  require GUS::Model::DoTS::ProteinGOProcess;
  require GUS::Model::DoTS::ProteinGOComponent;
  require GUS::Model::DoTS::ProteinGOFunction;

It looks like they have not been converted to GUS 3.0 yet
(with a strong hint in TASK_GoAnnotation(): ### NOTE: NOT YET UPDATED).
I'm willing to take a shot at updating these, but I don't
know where to find them (and what's involved in converting 
2.0 to 3.0 so I should be careful about volunteering ;-)

Terry