gusdev-gusdev — Topics concerning GUS development

[GUSDEV] RAD Study Annotator release 2.0.0 (compatible with GUS 3.5) is out

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

Apologies if you receive this message multiple times, it is sent to 
various mailing lists.

This is to let you know that a release of the RAD Study-Annotator 
compatible with GUS 3.5 is now available at 
http://www.cbil.upenn.edu/downloads/RAD/
This is in the tarball named RADSA_2.0.0.tar.gz

In this tarball you will find a README_2.0.0 file with detailed 
instructions on installation and pointers to further instructions and 
dump files to load bootstrap data.
Elisabetta

[GUSDEV] Re: RAD Study-Annotator issues (Junmin Liu)

[Amruta J. <am...@st...>]

Hi Junmin,

All OCI calls work fine with php+Oracle 10g (so php was compiled with the 
rite support Oracle options) but ora_ calls fail silently. It seems that 
ora_ calls which were earlier deprecated are not supported.

I may have to change the ora_ calls to OCI to have the Study Annotator 
working. What all problems did you face while using OCI?

thanks,
Amruta

>
>   1. Re: RAD Study-Annotator issues (Junmin Liu)
>
> Hi, Amruta,
> Yes, the OCI is more modern oracle php lib. At one point I migrated the
> code to use OCI, but I had to revert them back due to some reasons I 
> cann't
> remember for now. Sorry about that, it could be that I cann't find a way
> to "fetch clob datatype from Oracle using OCI fucntion".
>
> Anyway, could you please check your php config? What is the options you
> use to compile PHP? Do you have the following two options:
>
>  --with-oracle=/path/to/oracle/home/dir
>  --with-oci8=/path/to/oracle/home/dir
>
>
> ---junmin
>

Re: [GUSDEV] ant problem on install?

[Chris T. <cmt...@gm...>]

when I run ant cmd from cmd line I get:

\Exception in thread "main" java.lang.NoClassDefFoundError:
org/apache/tools/ant/launch/Launcher

does this mean I need certain libraries on my $CLASSPATH? Which ones and
where are they?

I'm using 2.4.21-15.EL RedHat but have installed my own java and ant becaus=
e
I don't have root.

On 11/10/05, Angel Pizarro <an...@ma...> wrote:
>
> Try:
>
> $ build GUS install -append -returnErrStatus -installDBSchema
>
> This may give you a useful error message. Other than that, try
> un-commenting line line 41 in build.pl to see the ant command that is
> run and try cutting/pasting this command to get even more verbose output
> from straight from ant.
>
>
>
>
> Chris Topinka wrote:
>
> >
> PATH=3D/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/oracle/usr/=
local/apache-
> ant-1.6.5
> /bin:/home/oracle/GUS/gus_home/bin:/home/oracle/GUS/project_home/install/=
bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/orac=
le/product/9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin
> >
> >
> > this is my $PATH
> >
> > which java and which ant now returns the bins that I want and
> > installed in my home (I don't have root unfortunately). Before which
> > had old ant and no java.
> >
> > Now when I run build it exits immediately with no output.
> >
> > What does build require exactly? In what order?
> >
> > Is there a simpler way to get the xml schema onto my oracle db?
> >
> > Thanks
> > On 11/8/05, *msa...@pc... <mailto:msa...@pc...>*
> > <msa...@pc... <mailto:msa...@pc...>> wrote:
> >
> > Hi Chris,
> >
> > I would double check your version of Ant. I believe 1.6.2 is
> > required. Also,
> > if on Linux, make sure you're using the copy you think you are--
> > RedHat for a
> > while included a non-compatible version of Ant. Do 'which ant' to
> > display the
> > version in use. Also, make sure there is no /etc/ant.conf file.
> >
> > --Mike
> >
> > Quoting Chris Topinka <cmt...@gm...
> > <mailto:cmt...@gm...>>:
> >
> > > When I run:
> > >
> > > build GUS install -append -installDBSchema
> > >
> > > I immediately get:
> > > ant [options] [target [target2 [target3] ...]]
> > >
> > > and then 'build' terminates
> > >
> > > I couldn't find anything in the list archives with this output.
> > Is there a
> > > better way to search for this in the archives for future reference?
> > >
> > > I installed Ant myself, so this could very likely be the problem.
> > > --
> > > Christopher M. Topinka
> > > NLM-BHIRT Predoctoral Fellow in Computer Science
> > > 113 Life Sciences Center
> > > University of Missouri
> > > Columbia, MO 65211
> > > (573)-823-0616
> > > cmt...@mi... <mailto:cmt...@mi...>
> > >
> >
> >
> >
> >
> >
> >
> > --
> > Christopher M. Topinka
> > NLM-BHIRT Predoctoral Fellow in Computer Science
> > 113 Life Sciences Center
> > University of Missouri
> > Columbia, MO 65211
> > (573)-823-0616
> > cmt...@mi... <mailto:cmt...@mi...>
>
>
>
> --
>
> Angel Pizarro
> Director, Bioinformatics Facility
> Institute for Translational Medicine and Therapeutics
> University of Pennsylvania
> 806 BRB II/III
> 421 Curie Blvd.
> Philadelphia, PA 19104-6160
>
> P: 215-573-3736
> F: 215-573-9004
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>



--
Christopher M. Topinka
NLM-BHIRT Predoctoral Fellow in Computer Science
113 Life Sciences Center
University of Missouri
Columbia, MO 65211
(573)-823-0616
cmt...@mi...

Re: [GUSDEV] ant problem on install?

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

Try:

$ build  GUS install -append -returnErrStatus -installDBSchema

This may give you a useful error message. Other than that, try 
un-commenting line line 41 in build.pl to see the ant command that is 
run and try cutting/pasting this command to get even more verbose output 
from straight from ant.




Chris Topinka wrote:

> PATH=/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/oracle/usr/local/apache-ant-1.6.5/bin:/home/oracle/GUS/gus_home/bin:/home/oracle/GUS/project_home/install/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/oracle/product/9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin 
>
>
> this is my $PATH
>
> which java and which ant now returns the bins that I want and 
> installed in my home (I don't have root unfortunately).  Before which 
> had old ant and no java.
>
> Now when I run build it exits immediately with no output.
>
> What does build require exactly?  In what order?
>
> Is there a simpler way to get the xml schema onto my oracle db?
>
> Thanks
> On 11/8/05, *msa...@pc... <mailto:msa...@pc...>* 
> <msa...@pc... <mailto:msa...@pc...>> wrote:
>
>     Hi Chris,
>
>     I would double check your version of Ant.  I believe 1.6.2 is
>     required.  Also,
>     if on Linux, make sure you're using the copy you think you are--
>     RedHat for a
>     while included a non-compatible version of Ant.  Do 'which ant' to
>     display the
>     version in use.  Also, make sure there is no /etc/ant.conf file.
>
>     --Mike
>
>     Quoting Chris Topinka <cmt...@gm...
>     <mailto:cmt...@gm...>>:
>
>     > When I run:
>     >
>     > build GUS install -append -installDBSchema
>     >
>     > I immediately get:
>     > ant [options] [target [target2 [target3] ...]]
>     >
>     > and then 'build' terminates
>     >
>     > I couldn't find anything in the list archives with this output.
>     Is there a
>     > better way to search for this in the archives for future reference?
>     >
>     > I installed Ant myself, so this could very likely be the problem.
>     > --
>     > Christopher M. Topinka
>     > NLM-BHIRT Predoctoral Fellow in Computer Science
>     > 113 Life Sciences Center
>     > University of Missouri
>     > Columbia, MO 65211
>     > (573)-823-0616
>     > cmt...@mi... <mailto:cmt...@mi...>
>     >
>
>
>
>
>
>
> -- 
> Christopher M. Topinka
> NLM-BHIRT Predoctoral Fellow in Computer Science
> 113 Life Sciences Center
> University of Missouri
> Columbia, MO 65211
> (573)-823-0616
> cmt...@mi... <mailto:cmt...@mi...> 



-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

Re: [GUSDEV] ant problem on install?

[Chris T. <cmt...@gm...>]

dbiDsn=3D*perl_dbi_string*[image: 2]
jdbcDsn=3D*jdbc_conection_string

Are these fields in the config file necessary for install to work?=20
How do I know what these are?

I installed my own oracle.  how do i look these up?

thanks
*



On 11/10/05, Chris Topinka <cmt...@gm...> wrote:
>
>
> PATH=3D/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/oracle/usr/=
local/apache-
> ant-1.6.5/bin:/home/oracle/GUS/gus_home/bin:/home/oracle/GUS/project_home=
/install/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:=
/opt/oracle/product/9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin
>
>
> this is my $PATH
>
> which java and which ant now returns the bins that I want and installed i=
n
> my home (I don't have root unfortunately). Before which had old ant and n=
o
> java.
>
> Now when I run build it exits immediately with no output.
>
> What does build require exactly? In what order?
>
> Is there a simpler way to get the xml schema onto my oracle db?
>
> Thanks
> On 11/8/05, msa...@pc... <msa...@pc... > wrote:
> >
> > Hi Chris,
> >
> > I would double check your version of Ant. I believe 1.6.2 is required.
> > Also,
> > if on Linux, make sure you're using the copy you think you are-- RedHat
> > for a
> > while included a non-compatible version of Ant. Do 'which ant' to
> > display the
> > version in use. Also, make sure there is no /etc/ant.conf file.
> >
> > --Mike
> >
> > Quoting Chris Topinka <cmt...@gm...>:
> >
> > > When I run:
> > >
> > > build GUS install -append -installDBSchema
> > >
> > > I immediately get:
> > > ant [options] [target [target2 [target3] ...]]
> > >
> > > and then 'build' terminates
> > >
> > > I couldn't find anything in the list archives with this output. Is
> > there a
> > > better way to search for this in the archives for future reference?
> > >
> > > I installed Ant myself, so this could very likely be the problem.
> > > --
> > > Christopher M. Topinka
> > > NLM-BHIRT Predoctoral Fellow in Computer Science
> > > 113 Life Sciences Center
> > > University of Missouri
> > > Columbia, MO 65211
> > > (573)-823-0616
> > > cmt...@mi...
> > >
> >
> >
> >
> >
>
>
> --
> Christopher M. Topinka
> NLM-BHIRT Predoctoral Fellow in Computer Science
> 113 Life Sciences Center
> University of Missouri
> Columbia, MO 65211
> (573)-823-0616
> cmt...@mi...
>



--
Christopher M. Topinka
NLM-BHIRT Predoctoral Fellow in Computer Science
113 Life Sciences Center
University of Missouri
Columbia, MO 65211
(573)-823-0616
cmt...@mi...

Re: [GUSDEV] ant problem on install?

[Chris T. <cmt...@gm...>]

PATH=3D/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/oracle/usr/lo=
cal/apache-
ant-1.6.5
/bin:/home/oracle/GUS/gus_home/bin:/home/oracle/GUS/project_home/install/bi=
n:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/oracle=
/product/9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin

this is my $PATH

which java and which ant now returns the bins that I want and installed in
my home (I don't have root unfortunately). Before which had old ant and no
java.

Now when I run build it exits immediately with no output.

What does build require exactly? In what order?

Is there a simpler way to get the xml schema onto my oracle db?

Thanks
On 11/8/05, msa...@pc... <msa...@pc...> wrote:
>
> Hi Chris,
>
> I would double check your version of Ant. I believe 1.6.2 is required.
> Also,
> if on Linux, make sure you're using the copy you think you are-- RedHat
> for a
> while included a non-compatible version of Ant. Do 'which ant' to display
> the
> version in use. Also, make sure there is no /etc/ant.conf file.
>
> --Mike
>
> Quoting Chris Topinka <cmt...@gm...>:
>
> > When I run:
> >
> > build GUS install -append -installDBSchema
> >
> > I immediately get:
> > ant [options] [target [target2 [target3] ...]]
> >
> > and then 'build' terminates
> >
> > I couldn't find anything in the list archives with this output. Is ther=
e
> a
> > better way to search for this in the archives for future reference?
> >
> > I installed Ant myself, so this could very likely be the problem.
> > --
> > Christopher M. Topinka
> > NLM-BHIRT Predoctoral Fellow in Computer Science
> > 113 Life Sciences Center
> > University of Missouri
> > Columbia, MO 65211
> > (573)-823-0616
> > cmt...@mi...
> >
>
>
>
>


--
Christopher M. Topinka
NLM-BHIRT Predoctoral Fellow in Computer Science
113 Life Sciences Center
University of Missouri
Columbia, MO 65211
(573)-823-0616
cmt...@mi...

Re: [GUSDEV] RAD Study-Annotator issues

[Junmin L. <ju...@pc...>]

Hi, Amruta,
Yes, the OCI is more modern oracle php lib. At one point I migrated the 
code to use OCI, but I had to revert them back due to some reasons I cann't 
remember for now. Sorry about that, it could be that I cann't find a way 
to "fetch clob datatype from Oracle using OCI fucntion".

Anyway, could you please check your php config? What is the options you 
use to compile PHP? Do you have the following two options:

  --with-oracle=/path/to/oracle/home/dir
  --with-oci8=/path/to/oracle/home/dir


---junmin




On Wed, 9 Nov 2005, Amruta Joshi wrote:

> Hi,
>
> We have installed GUS & have some basic data in it. We are using Oracle 10g 
> (Release 10.1).
>
> I have compiled the Study-Annotator for entering study-related data. However, 
> all the ora_ calls in the php files (likeora_logon, ora_getColumn etc.) fail. 
> I keep getting the error:
>   Fatal error: Call to undefined function: ora_logon()
>
> The function ociLogon works just fine. It seems that Oracle 10g supports only 
> OCI calls and not ora_ functions, which means I may have to rewrite chunks of 
> code that use ora_ calls.
>   Is there a better alternative to this?
>   Is Study-Annotator also made available with the new OCI calls?
> I'm using the Study-Annotator source code from 
> http://www.cbil.upenn.edu/downloads/RAD/
>
> Please reply soon, we need to get this working asap.
>
> thanks,
> Amruta
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] SVN questions

[Mark S. H. <mh...@ug...>]

On Nov 9, 2005, at 7:05 AM, Henrique Juc=E1 wrote:

> Hi all,
>
>
> What is that GusTrunk/ inside que repos?
>


On Nov 3, 2005, at 3:17 PM, Michael Saffitz wrote:
>
> Just a quick note:
>
> You may now do:
>
> svn co https://www.cbil.upenn.edu/svn/gus/gusTrunk GUS
>
> This will automatically setup a shell GUS environment in the =20
> directory GUS consisting of an empty gus_home (with empty config =20
> directory), and a project_home directory with local checkouts of =20
> each of GusAppFramework, GusSchema, install, and CBIL trunks.  =20
> There is also a env.bash file that will configure your =20
> environment.  You must either edit this file and supply the =20
> GUS_BASE, or source this file from WITHIN the GUS directory.
>
> This eliminates the needs to do the four checkouts separately.  =20
> This will also allow you to do a svn update in the GUS directory to =20=

> update all four projects simultaneously.
>
> All that is then necessary for a gus build is to copy and edit the =20
> project_home/install/gus.config.sample file to gus_home/config/=20
> gus.config; and then do build GUS install -append.
>
> Brought to you by the magic of Subversion externals.
>
> --Mike

[GUSDEV] SVN questions

[<hen...@gm...>]

Hi all,


What is that GusTrunk/ inside que repos?


Thanks,

--
Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] RAD Study-Annotator issues

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

Hi Amruta,
the RAD study annotator (RADSA) tarballs currently available at the 
donwload site you indicated below are both for previous version of GUS (< 
3.5). A tarball for a RADSA compatible with GUS 3.5 will be released 
probably next week or early the following week and I'll send an 
announcement as soon as that occurs.
Regarding the specific error and Oracle, I had a look at the code for the 
function that is used to connect to the db in the upcoming release (which 
we have been testing and using here in the past month and which works for 
us). 
It appears that it still uss ora_logon (albeit I see a commented out 
OCILogon call). I'll let Junmin, here cc-ed comment on this.
Elisabetta

---

On Wed, 9 Nov 2005, Amruta Joshi wrote:

> Hi,
>
> We have installed GUS & have some basic data in it. We are using Oracle 10g 
> (Release 10.1).
>
> I have compiled the Study-Annotator for entering study-related data. However, 
> all the ora_ calls in the php files (likeora_logon, ora_getColumn etc.) fail. 
> I keep getting the error:
>   Fatal error: Call to undefined function: ora_logon()
>
> The function ociLogon works just fine. It seems that Oracle 10g supports only 
> OCI calls and not ora_ functions, which means I may have to rewrite chunks of 
> code that use ora_ calls.
>   Is there a better alternative to this?
>   Is Study-Annotator also made available with the new OCI calls?
> I'm using the Study-Annotator source code from 
> http://www.cbil.upenn.edu/downloads/RAD/
>
> Please reply soon, we need to get this working asap.
>
> thanks,
> Amruta
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] RAD Study-Annotator issues

[Amruta J. <am...@st...>]

Hi,

We have installed GUS & have some basic data in it. We are using Oracle 10g 
(Release 10.1).

I have compiled the Study-Annotator for entering study-related data. 
However, all the ora_ calls in the php files (likeora_logon, ora_getColumn 
etc.) fail. I keep getting the error:
    Fatal error: Call to undefined function: ora_logon()

The function ociLogon works just fine. It seems that Oracle 10g supports 
only OCI calls and not ora_ functions, which means I may have to rewrite 
chunks of code that use ora_ calls.
    Is there a better alternative to this?
    Is Study-Annotator also made available with the new OCI calls?
I'm using the Study-Annotator source code from 
http://www.cbil.upenn.edu/downloads/RAD/

Please reply soon, we need to get this working asap.

thanks,
Amruta

Re: [GUSDEV] ant problem on install?

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

Hi Chris,

I would double check your version of Ant.  I believe 1.6.2 is required.  Also,
if on Linux, make sure you're using the copy you think you are-- RedHat for a
while included a non-compatible version of Ant.  Do 'which ant' to display the
version in use.  Also, make sure there is no /etc/ant.conf file.

--Mike

Quoting Chris Topinka <cmt...@gm...>:

> When I run:
>
> build GUS install -append -installDBSchema
>
> I immediately get:
> ant [options] [target [target2 [target3] ...]]
>
> and then 'build' terminates
>
> I couldn't find anything in the list archives with this output. Is there a
> better way to search for this in the archives for future reference?
>
> I installed Ant myself, so this could very likely be the problem.
> --
> Christopher M. Topinka
> NLM-BHIRT Predoctoral Fellow in Computer Science
> 113 Life Sciences Center
> University of Missouri
> Columbia, MO 65211
> (573)-823-0616
> cmt...@mi...
>

[GUSDEV] ant problem on install?

[Chris T. <cmt...@gm...>]

When I run:

build GUS install -append -installDBSchema

I immediately get:
 ant [options] [target [target2 [target3] ...]]

and then 'build' terminates

I couldn't find anything in the list archives with this output. Is there a
better way to search for this in the archives for future reference?

I installed Ant myself, so this could very likely be the problem.
--
Christopher M. Topinka
NLM-BHIRT Predoctoral Fellow in Computer Science
113 Life Sciences Center
University of Missouri
Columbia, MO 65211
(573)-823-0616
cmt...@mi...

Re: [GUSDEV] WDK error

[<hen...@gm...>]

Hi Thomas,


I have the same file as you do.

 head $GUS_HOME/data/WDKToySite/Model/testTables/WDKTestEst
row_project_id number(10) not null,     est_id number(10) not null,  =20
 na_sequence_id number(10) not null,    clone_id number(10),  =20
library_id number(5) not null,  dbest_id_est number(12),     =20
accession varchar(20),  quality_start number(12) not null,  =20
quality_stop number(12), seq_length number(12)
10      9644241 20103105                9602    2398182 AI579851     =20
 1       0     0
10      9644243 20103107                9602    2398184 AI579853     =20
 1       0     0
10      9644244 20103108                9602    2398185 AI579854     =20
 1       0     0
10      9644248 20103112                9602    2398189 AI579858     =20
 1       0     0
10      9644249 20103113                9602    2398190 AI579859     =20
 1       0     0
10      9644251 20103115                9602    2398192 AI579861     =20
 1       0     0
10      9644261 20103125                9602    2398202 AI579871     =20
 1       0     0
10      9644273 20103137                9602    2398214 AI579883     =20
 1       0     0
10      9644283 20901075                9603    3264539 AW119237    =20
1       0     0

And I got the same error.

[juca1@kineto3 project_home]$ wdkTestDb -model toyModel -drop
Dropping existing table usertest.WDKTestEst
[juca1@kineto3 project_home]$ wdkTestDb -model toyModel -create

Loading table usertest.WDKTestEst to database from file

ERROR: column "row_project_id" is of type numeric but expression is of
type character varying
java.sql.SQLException: ERROR: column "row_project_id" is of type
numeric but expression is of type character varying
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(Qu=
eryExecutorImpl.java:1471)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExe=
cutorImpl.java:1256)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorIm=
pl.java:175)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc=
2Statement.java:392)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(Abs=
tractJdbc2Statement.java:330)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(Abstra=
ctJdbc2Statement.java:282)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdat=
e(DelegatingPreparedStatement.java:233)
        at org.gusdb.wdk.model.implementation.SqlUtils.getResultSet(SqlUtil=
s.java:51)
        at org.gusdb.wdk.model.test.TestDBManager.main(TestDBManager.java:1=
17)

Thanks for the attention,

Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] DBD connect error

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

Hi Juan,
the gus.propertios file is no longer used. See email from Mike in this 
regard on Oct 28.
Elisabetta

---

On Mon, 7 Nov 2005, Juan Carlos Perin wrote:

> Hello,
>
> I'm having DBD connection problems.  I assume this is because of DBIdsn not
> set properly in my gus.properties file.  Should I be trying a more specific
> name?  The error is:
>
> ##GUS::ObjRelP::DbiDbHandle connect('orcl','gususer',...) failed: ORA-12514:
> ##TNS:listener does not currently know of service requested in connect
> ##descriptor (DBD ERROR: OCIServerAttach) at
> ##/home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 165
> ##Can't bless non-reference value at
> ##/home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
>
>
>
> The latter half of my gus.properties looks like this:
>
>
>
> ##coreSchemaName=CORE
> ##userName=dba
> ##group=dba
> ##project=Database administration
> ##dbiDsn=dbi:Oracle:orcl
>
>
>
>
> The listener is running fine, the output of the start looks like this:
>
>
>
>
> #########################################################################
> LSNRCTL for Linux: Version 10.2.0.1.0 - Production on 07-NOV-2005 12:18:21
>
> Copyright (c) 1991, 2005, Oracle.  All rights reserved.
>
> Starting /u01/app/oracle/oracle/product/10.2.0/db_1/bin/tnslsnr: please
> wait...
>
> TNSLSNR for Linux: Version 10.2.0.1.0 - Production
> System parameter file is
> /u01/app/oracle/oracle/product/10.2.0/db_1/network/admin/listener.ora
> Log messages written to
> /u01/app/oracle/oracle/product/10.2.0/db_1/network/log/listener.log
> Listening on: (DESCRIPTION=(ADDRESS=(PROTOCOL=ipc)(KEY=EXTPROC1)))
> Listening on:
> (DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=bioinformatics-server.res.chop.edu
> )(PORT=1521)))
>
> Connecting to (DESCRIPTION=(ADDRESS=(PROTOCOL=IPC)(KEY=EXTPROC1)))
> STATUS of the LISTENER
> ------------------------
> Alias                     LISTENER
> Version                   TNSLSNR for Linux: Version 10.2.0.1.0 - Production
> Start Date                07-NOV-2005 12:18:21
> Uptime                    0 days 0 hr. 0 min. 0 sec
> Trace Level               off
> Security                  ON: Local OS Authentication
> SNMP                      OFF
> Listener Parameter File
> /u01/app/oracle/oracle/product/10.2.0/db_1/network/admin/listener.ora
> Listener Log File
> /u01/app/oracle/oracle/product/10.2.0/db_1/network/log/listener.log
> Listening Endpoints Summary...
>  (DESCRIPTION=(ADDRESS=(PROTOCOL=ipc)(KEY=EXTPROC1)))
>
> (DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=bioinformatics-server.res.chop.edu
> )(PORT=1521)))
> Services Summary...
> Service "PLSExtProc" has 1 instance(s).
>  Instance "PLSExtProc", status UNKNOWN, has 1 handler(s) for this
> service...
> The command completed successfully
>
>
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] DBD connect error

[Juan C. P. <bi...@ge...>]

Hello,

I'm having DBD connection problems.  I assume this is because of DBIdsn not
set properly in my gus.properties file.  Should I be trying a more specific
name?  The error is:

##GUS::ObjRelP::DbiDbHandle connect('orcl','gususer',...) failed: ORA-12514:
##TNS:listener does not currently know of service requested in connect
##descriptor (DBD ERROR: OCIServerAttach) at
##/home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 165
##Can't bless non-reference value at
##/home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.



The latter half of my gus.properties looks like this:



##coreSchemaName=CORE
##userName=dba
##group=dba
##project=Database administration
##dbiDsn=dbi:Oracle:orcl




The listener is running fine, the output of the start looks like this:




#########################################################################
LSNRCTL for Linux: Version 10.2.0.1.0 - Production on 07-NOV-2005 12:18:21

Copyright (c) 1991, 2005, Oracle.  All rights reserved.

Starting /u01/app/oracle/oracle/product/10.2.0/db_1/bin/tnslsnr: please
wait...

TNSLSNR for Linux: Version 10.2.0.1.0 - Production
System parameter file is
/u01/app/oracle/oracle/product/10.2.0/db_1/network/admin/listener.ora
Log messages written to
/u01/app/oracle/oracle/product/10.2.0/db_1/network/log/listener.log
Listening on: (DESCRIPTION=(ADDRESS=(PROTOCOL=ipc)(KEY=EXTPROC1)))
Listening on: 
(DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=bioinformatics-server.res.chop.edu
)(PORT=1521)))

Connecting to (DESCRIPTION=(ADDRESS=(PROTOCOL=IPC)(KEY=EXTPROC1)))
STATUS of the LISTENER
------------------------
Alias                     LISTENER
Version                   TNSLSNR for Linux: Version 10.2.0.1.0 - Production
Start Date                07-NOV-2005 12:18:21
Uptime                    0 days 0 hr. 0 min. 0 sec
Trace Level               off
Security                  ON: Local OS Authentication
SNMP                      OFF
Listener Parameter File
/u01/app/oracle/oracle/product/10.2.0/db_1/network/admin/listener.ora
Listener Log File  
/u01/app/oracle/oracle/product/10.2.0/db_1/network/log/listener.log
Listening Endpoints Summary...
  (DESCRIPTION=(ADDRESS=(PROTOCOL=ipc)(KEY=EXTPROC1)))
  
(DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=bioinformatics-server.res.chop.edu
)(PORT=1521)))
Services Summary...
Service "PLSExtProc" has 1 instance(s).
  Instance "PLSExtProc", status UNKNOWN, has 1 handler(s) for this
service...
The command completed successfully

RE: [GUSDEV] WDK error

[Y. T. G. <yg...@pc...>]

Hi Henrique,
1) Try wdkTestDb -model toyModel -drop before create
2) look your data file.=20
Below is what I have:
head $GUS_HOME/data/WDKToySite/Model/testTables/WDKTestEst
row_project_id number(10) not null,     est_id number(10) not null,
na_sequence_id number(10) not null,     clone_id number(10),library_id
number(5) not null,  dbest_id_est number(12),        accession
varchar(20),  quality_start number(12) not null,      quality_stop
number(12),    seq_length number(12)
10      9644241 20103105                9602    2398182 AI579851
1       0       0
10      9644243 20103107                9602    2398184 AI579853
1       0       0
10      9644244 20103108                9602    2398185 AI579854
1       0       0
10      9644248 20103112                9602    2398189 AI579858
1       0       0
10      9644249 20103113                9602    2398190 AI579859
1       0       0
10      9644251 20103115                9602    2398192 AI579861
1       0       0
10      9644261 20103125                9602    2398202 AI579871
1       0       0
10      9644273 20103137                9602    2398214 AI579883
1       0       0
10      9644283 20901075                9603    3264539 AW119237
1       0       0

-Thomas

> -----Original Message-----
> From: gus...@li...=20
> [mailto:gus...@li...] On Behalf=20
> Of Henrique Juc
> Sent: Thursday, November 03, 2005 2:31 PM
> To: Gusdev gusdev-gusdev
> Cc: Y. Thomas Gan
> Subject: Re: [GUSDEV] WDK error
>=20
>=20
> Thanks fo the help.
>=20
> I did as you instructed, and downloaded WDK-stable from the=20
> homepage. Everything went well till the same step.
>=20
>=20
>  $ wdkTestDb -model toyModel -create
>=20
> Loading table usertest.WDKTestEst to database from file
>=20
> ERROR: column "row_project_id" is of type numeric but=20
> expression is of type character varying
> java.sql.SQLException: ERROR: column "row_project_id" is of=20
> type numeric but expression is of type character varying
>         at=20
> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(
> QueryExecutorImpl.java:1471)
>         at=20
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryE
> xecutorImpl.java:1256)
>         at=20
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutor
> Impl.java:175)
>         at=20
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJd
> bc2Statement.java:392)
>         at=20
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(A
> bstractJdbc2Statement.java:330)
> at=20
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(Abst
> ractJdbc2Statement.java:282)
>        at=20
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpd
> ate(DelegatingPreparedStatement.java:233)
>         at=20
> org.gusdb.wdk.model.implementation.SqlUtils.getResultSet(SqlUt
> ils.java:51)
>         at=20
> org.gusdb.wdk.model.test.TestDBManager.main(TestDBManager.java:117)
>=20
> Did I forget anything?
>=20
>=20
>  Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>=20
> "As soon as you concern yourself with the "good" and "bad" of=20
> your fellows, you create an opening in your heart for=20
> maliciousness to enter. Testing, competing with, and=20
> criticizing others weaken and defeat you."
>=20
> Morihei Ueshiba, O-Sensei (1883-1969)
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App=20
> Server. Download it for free - -and be entered to win a 42"=20
> plasma tv or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
>=20
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>=20

[GUSDEV] GUS Checkout Shortcut

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

Just a quick note:

You may now do:

svn co https://www.cbil.upenn.edu/svn/gus/gusTrunk GUS

This will automatically setup a shell GUS environment in the  
directory GUS consisting of an empty gus_home (with empty config  
directory), and a project_home directory with local checkouts of each  
of GusAppFramework, GusSchema, install, and CBIL trunks.  There is  
also a env.bash file that will configure your environment.  You must  
either edit this file and supply the GUS_BASE, or source this file  
from WITHIN the GUS directory.

This eliminates the needs to do the four checkouts separately.  This  
will also allow you to do a svn update in the GUS directory to update  
all four projects simultaneously.

All that is then necessary for a gus build is to copy and edit the  
project_home/install/gus.config.sample file to gus_home/config/ 
gus.config; and then do build GUS install -append.

Brought to you by the magic of Subversion externals.

--Mike

(Note:  This is for our new server.  DNS propagation changes may  
cause this to not work for some people for about 24 hours).

Re: [GUSDEV] Additions to GUS Schema

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

Hi Eric,
Thanks very much for bringing this up and willingness to contribute.  
A mechanism we've been using for schema changes so far has been:
1. raise issue on gusdev list to see if existing solution exists and  
potential new solutions
2. enter proposal on GUS bug tracker
3. schema owner (e.g., I'm the owner for DoTS) responds too proposal  
until agreed upon solution is found and sets milestone (next patch if  
won't break code, next release if will break code. etc)
4. GUS administrator (currently Mike Saffitz) sends out proposed  
patch (e.g., 3.5.1) or release (e.g., 3.6) to gusdev list for final  
review and then applies.

Jian has already used this mechanism that has resulted in changes in  
3.5.1 and 3.6. Presumably something like this can work for other GUS  
components.

How does this sound?

Cheers,
Chris

On Nov 3, 2005, at 1:46 PM, Eric E. Snyder wrote:

>> From: Jian Lu <jl...@vb...>
>> We have EC numbers loaded into SRes.EnzymeClass and TIGRFAM ids  
>> into SRes.ExternalDatabaseEntry, but we couldn't find a place  
>> within GUS schema to store the relationship of them.
>
> This brings up the larger question of how best to integrate 3rd  
> party additions into future GUS releases.
>
> Steve Fischer <sfi...@pc...> wrote:
> > this seems reasonable to me.
>
> Is is possible to achieve a consensus on how best to address  
> limitations such as the one Jian Lu's code addresses so that a  
> robust solution can be devised and included in later releases?   
> Perhaps other groups have developed similar (or perhaps totally  
> different) solutions.  I would like to see more discussions of this  
> type in this mailing list.
>
> We would be more than happy to contribute our enhancements if they  
> could be vetted by the GUS team (and other interested parties) and  
> incorporated into the distribution.  While I don't presume that GUS  
> was intended to be a BioPerl-style collaborative project, we would  
> really like to contribute.  What can we do to help this happen?
>
> Cheers,
> -- 
> Eric E. Snyder, Ph.D.
> Virginia Bioinformatics Institute
> Virginia Polytechnic Institute and State University
> Blacksburg, VA 24061-0447
> <esnyder.vcf>

Re: [GUSDEV] WDK error

[<hen...@gm...>]

Thanks fo the help.

I did as you instructed, and downloaded WDK-stable from the homepage.
Everything went well till the same step.


 $ wdkTestDb -model toyModel -create

Loading table usertest.WDKTestEst to database from file

ERROR: column "row_project_id" is of type numeric but expression is of
type character varying
java.sql.SQLException: ERROR: column "row_project_id" is of type
numeric but expression is of type character varying
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(Qu=
eryExecutorImpl.java:1471)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExe=
cutorImpl.java:1256)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorIm=
pl.java:175)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc=
2Statement.java:392)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(Abs=
tractJdbc2Statement.java:330)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2S=
tatement.java:282)
       at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate=
(DelegatingPreparedStatement.java:233)
        at org.gusdb.wdk.model.implementation.SqlUtils.getResultSet(SqlUtil=
s.java:51)
        at org.gusdb.wdk.model.test.TestDBManager.main(TestDBManager.java:1=
17)

Did I forget anything?


 Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] Additions to GUS Schema

[Eric E. S. <es...@vb...>]

> From: Jian Lu <jl...@vb...>
> We have EC numbers loaded into SRes.EnzymeClass and TIGRFAM ids into 
> SRes.ExternalDatabaseEntry, but we couldn't find a place within GUS 
> schema to store the relationship of them. 

This brings up the larger question of how best to integrate 3rd party 
additions into future GUS releases.

Steve Fischer <sfi...@pc...> wrote:
 > this seems reasonable to me.

Is is possible to achieve a consensus on how best to address limitations 
such as the one Jian Lu's code addresses so that a robust solution can 
be devised and included in later releases?  Perhaps other groups have 
developed similar (or perhaps totally different) solutions.  I would 
like to see more discussions of this type in this mailing list.

We would be more than happy to contribute our enhancements if they could 
be vetted by the GUS team (and other interested parties) and 
incorporated into the distribution.  While I don't presume that GUS was 
intended to be a BioPerl-style collaborative project, we would really 
like to contribute.  What can we do to help this happen?

Cheers,
-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447

Re: [GUSDEV] Re: [ApiDB] SVN Changes Again

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

Hi Mark,

It may be that the DNS changes haven't propagated down there yet.  If  
www.cbil.upenn.edu doesn't point to 128.91.133.130, then you're using  
the old DNS.

--Mike

On Nov 3, 2005, at 12:05 PM, Mark Heiges wrote:

> I'm not able to get it to work. What am I doing wrong?
>
> svn switch --relocate https://svn.cbil.upenn.edu/
> https://www.cbil.upenn.edu/svn .
> svn: PROPFIND request failed
> on '/svn/gus/GusAppFramework/trunk'
> svn: PROPFIND of '/svn/gus/GusAppFramework/trunk': 405
> Method Not Allowed (https://www.cbil.upenn.edu)
>
> ## or:
>
> svn co https://www.cbil.upenn.edu/svn/gus/GusAppFramework/tru
> nk GUS
> svn: PROPFIND request failed
> on '/svn/gus/GusAppFramework/trunk'
> svn: PROPFIND of '/svn/gus/GusAppFramework/trunk': 405
> Method Not Allowed (https://www.cbil.upenn.edu)
>
>
> ---- Original message ----
>
>> Date: Thu, 3 Nov 2005 11:23:58 -0500
>> From: Michael Saffitz <msa...@pc...>
>> Subject: [ApiDB] SVN Changes Again
>> To: ApiDB Project Mailing List <Ap...@pc...>,
>>
> cb...@pc..., Gusdev gusdev-gusdev <gusdev-
> gu...@li...>
>
>>
>>
>> All,
>>
>> I'm very sorry to announce one last round of Subversion URL
>>
> changes.
>
>> These are necessary due to routing conflicts on our new
>>
> webserver,
>
>> and a desire to continue to keep subversion traffic secure.
>>
>> You will need to make the following change in the root of
>>
> each local
>
>> checkout:
>>
>> svn switch --relocate https://svn.cbil.upenn.edu/ https://
>> www.cbil.upenn.edu/svn .
>>
>> Sorry for the inconvenience.
>>
>> --Mike
>> _______________________________________________
>> ApiDB mailing list
>> Ap...@pc...
>> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb
>>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.  
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] Re: [ApiDB] SVN Changes Again

[Mark H. <mh...@ug...>]

I'm not able to get it to work. What am I doing wrong?

svn switch --relocate https://svn.cbil.upenn.edu/ 
https://www.cbil.upenn.edu/svn .
svn: PROPFIND request failed 
on '/svn/gus/GusAppFramework/trunk'
svn: PROPFIND of '/svn/gus/GusAppFramework/trunk': 405 
Method Not Allowed (https://www.cbil.upenn.edu)

## or:

svn co https://www.cbil.upenn.edu/svn/gus/GusAppFramework/tru
nk GUS
svn: PROPFIND request failed 
on '/svn/gus/GusAppFramework/trunk'
svn: PROPFIND of '/svn/gus/GusAppFramework/trunk': 405 
Method Not Allowed (https://www.cbil.upenn.edu)


---- Original message ----
>Date: Thu, 3 Nov 2005 11:23:58 -0500
>From: Michael Saffitz <msa...@pc...>  
>Subject: [ApiDB] SVN Changes Again  
>To: ApiDB Project Mailing List <Ap...@pc...>, 
cb...@pc..., Gusdev gusdev-gusdev <gusdev-
gu...@li...>
>
>
>All,
>
>I'm very sorry to announce one last round of Subversion URL 
changes.   
>These are necessary due to routing conflicts on our new 
webserver,  
>and a desire to continue to keep subversion traffic secure.
>
>You will need to make the following change in the root of 
each local  
>checkout:
>
>svn switch --relocate https://svn.cbil.upenn.edu/ https:// 
>www.cbil.upenn.edu/svn .
>
>Sorry for the inconvenience.
>
>--Mike
>_______________________________________________
>ApiDB mailing list
>Ap...@pc...
>https://mail.pcbi.upenn.edu/mailman/listinfo/apidb

Re: [GUSDEV] LoadNRDB error

[<hen...@gm...>]

Thanks Michael, it worked. But shouldn't this lines from the --help be
updated then?

The help file from LoadNRDB prints:

  --dbiStr *string*

        server and machine for temp table, e.g.
        dbi:Oracle:host=3Derebus.pcbi.upenn.edu;sid=3Dgusdev

Shouldn't that line be corrected?

Another thing, I've been trying to update sres.externaldatabase table
with no success.

$ ga GUS::Supported::Plugin::InsertExternalDatabase --name tpg --commit

Thu Nov  3 14:07:35 2005        ARG     algoinvo        1
Thu Nov  3 14:07:35 2005        ARG     comment
Thu Nov  3 14:07:35 2005        ARG     commit  1
Thu Nov  3 14:07:35 2005        ARG     debug   0
Thu Nov  3 14:07:35 2005        ARG     group
Thu Nov  3 14:07:35 2005        ARG     gusconfigfile   /gus/GUS/gus.proper=
ties
Thu Nov  3 14:07:35 2005        ARG     help
Thu Nov  3 14:07:35 2005        ARG     helpHTML
Thu Nov  3 14:07:35 2005        ARG     name    tpg
Thu Nov  3 14:07:35 2005        ARG     project
Thu Nov  3 14:07:35 2005        ARG     sqlVerbose      0
Thu Nov  3 14:07:35 2005        ARG     user
Thu Nov  3 14:07:35 2005        ARG     verbose 0
Thu Nov  3 14:07:35 2005        ARG     veryVerbose     0
Thu Nov  3 14:07:35 2005        AlgInvocationId 63
Thu Nov  3 14:07:35 2005        COMMIT  commit on
DBD::Pg::st execute failed: ERROR:  duplicate key violates unique
constraint "pk_externaldatabase"

ERROR:

 SQL ERROR!! involving

    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
group_read, name, user_read, row_user_id, external_database_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
 Values: 1, 1, 1, tpg, 1, 1, 21, 0, 63, 1, 1, 1 at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(=
0x9100274)','\x{a}
SQL ERROR!! involving\x{a} \x{a}    INSERT INTO
SRes.ExternalDataba...') called at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHAS=
H(0x9100274)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x9691974)','ARRAY(0x96=
91a10)','\x{a}
   INSERT INTO SRes.ExternalDatabase (  group_write, other_...')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalD=
atabase=3DHASH(0x96831cc)','HASH(0x9682184)')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
        GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=3D=
HASH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
        GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=3DHA=
SH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDat=
abase.pm
line 103
        GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported=
::Plugin::InsertExternalDatabase=3DHASH(0x8e4b32c)','HASH(0x9616d54)')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 520
        eval {...} called at
/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 512
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExte=
rnalDatabase',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 430
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalData=
base')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 337
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalDatabase=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 246
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','ARRAY(0x8e46678)')
called at /gus/GUS/gus_home/bin/ga line 11

STACK TRACE:
 at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(=
0x9100274)','\x{a}
SQL ERROR!! involving\x{a} \x{a}    INSERT INTO
SRes.ExternalDataba...') called at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHAS=
H(0x9100274)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x9691974)','ARRAY(0x96=
91a10)','\x{a}
   INSERT INTO SRes.ExternalDatabase (  group_write, other_...')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalD=
atabase=3DHASH(0x96831cc)','HASH(0x9682184)')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
        GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=3D=
HASH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
        GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=3DHA=
SH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDat=
abase.pm
line 103
        GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported=
::Plugin::InsertExternalDatabase=3DHASH(0x8e4b32c)','HASH(0x9616d54)')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 520
        eval {...} called at
/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 512
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExte=
rnalDatabase',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 430
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalData=
base')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 337
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalDatabase=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 246
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','ARRAY(0x8e46678)')
called at /gus/GUS/gus_home/bin/ga line 11

I uploaded to this table a ExternalDatabases.xml archive, using
LoadGusXml. From what I could understand from that error, seems that
id was supplied to another entry (and indeed it was). I guess what is
happening is some kind of conflict between the entries I uploaded in
this tables and the new entries I'm trying to submit. I looked for any
conflicts among the entries I need to create (nr, tpe, tpd, tpg and a
few others) and the contents of the xml file, and I couldn't find any
duplicate entries.


Thanks again for the quick replies,


Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] SVN Changes Again

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

All,

I'm very sorry to announce one last round of Subversion URL changes.   
These are necessary due to routing conflicts on our new webserver,  
and a desire to continue to keep subversion traffic secure.

You will need to make the following change in the root of each local  
checkout:

svn switch --relocate https://svn.cbil.upenn.edu/ https:// 
www.cbil.upenn.edu/svn .

Sorry for the inconvenience.

--Mike