gusdev-gusdev — Topics concerning GUS development

Re: [GUSDEV] Building 3.5

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

marc-

can you provide the entire error message, including what you typed in.

thanks
steve

marc jackson wrote:

>Hello,
>
>I'm trying to install the GUS 3.5 framwork.
>I've modified the config file appopriately.
>
>Why am I getting the following error at the beginning
>of the build?
>
>error: java.lang.NullPointerException
>
>Regards,
>
>Marc
>
>_________________________________________________________________
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>
>
>-------------------------------------------------------------------------
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>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
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>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[GUSDEV] Building 3.5

[marc j. <de...@ho...>]

Hello,

I'm trying to install the GUS 3.5 framwork.
I've modified the config file appopriately.

Why am I getting the following error at the beginning
of the build?

error: java.lang.NullPointerException

Regards,

Marc

_________________________________________________________________
All-in-one security and maintenance for your PC.  Get a free 90-day trial! 
http://clk.atdmt.com/MSN/go/msnnkwlo0050000002msn/direct/01/?href=http://www.windowsonecare.com/?sc_cid=msn_hotmail

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[Fernan A. <fe...@ii...>]

+----[ an...@ne... <an...@ne...> (19.Oct.2006 13:13):
|
| Quoting Fernan Aguero <fe...@ii...>:
| 
| > So I'd say that you're safe using the trunk ... at least
| > until 3.6 comes out (because then the 3.6 branch will be
| > merged to trunk, correct?. At least this is how I now understand it.
| > Others please correct me if I'm wrong).

This is the idea I got after a discussion regarding the GUS
development process in the context of how it deals with the
version control repository (branches, tags, etc.) 

http://sourceforge.net/mailarchive/message.php?msg_id=12227127

| I've been re-reading the install documentation, and that's what made us take
| the decision of avoiding SVN in the first place:
| 
|   Warning
| 
|   Since the 3.5 release of GUS, the source repository is no longer the
|   preferred or recommended method for downloading GUS. The source repository
|   contains the most recent additions and changes to GUS, which may be
|   inconsistent with this and other documentation, and which may include changed
|   APIs that could cause data loss.
| 
| If this information no longer applies, that's probably a part that should be
| corrected, isn't it?

I've also re-read the docs, and also found this in the wiki:
http://www.gusdb.org/wiki/index.php/GusVersionBranch

"Up until release 3.5 GUS has not had any systematic or
rigorous approaches to releases. Instead, users of GUS
acquired the development version of the system directly from
the repository. This has the obvoius drawback that users
have unstable software, and no two users are likely to have
exactly the same software.

GUS will now adopt standard practice for releases.

[...]

Now that release 3.5 is complete, the trunk of the
repository is presumed to hold development that is aiming
towards release 3.6. When the feature set designated for 3.6
is complete, we create a branch in the repository tagged
"3.6". The trunk is now available for 3.7 development. The
3.6 branch undergoes final testing and corrections. When
that process is complete the branch is tagged with "3.6.0",
and source is bundled for distribution and made available on
the download site. Inevitably minor problems or "bugs" will
be unearthed by the users. As these are corrected, the
source is advanced through the 3.6.1, 3.6.2, etc. The branch
is tagged each time and the source rebundled for
distribution"

The question would now be:

is this still a proposal? Or is it being enforced as we
speak?


| > But in any case you can always checkout a snapshot from any point back in
| > time...
| 
| I've tried to, but just don't seem to be able to: gusTrunk is an empty
| container that relies on other external trunks for getting the real software.

Mmm ... 

| No matter what release I ask for, I always end up with the latest tree being
| checked out for these external sources. For instance, the command

yes, this seems to be the case.
| 
| svn co --revision {2006-04-11} https://www.cbil.upenn.edu/svn/gus/gusTrunk .
| 
| terminates with the following lines:
| 
| ------------------------------------------------------
| Fetching external item into 'project_home/install'
|  ...
| Checked out external at revision 5069.
| 
| 
| Fetching external item into 'project_home/GusSchema'
|  ...
| Checked out external at revision 5069.
| 
| Checked out revision 4752.
| ------------------------------------------------------

Indeed. Rev 4752 should be the one we fetched back in April,
but the gusTrunk container seems to be pointing to the latest
revision (5069) of GusApplication and GusSchema ...

I have just checked out a new snapshot using
svn co --revision "{2006-04-11}" https://www.cbil.upenn.edu/svn/gus/gusTrunk GUS
into a directory named gus-23Oct2006

and extracted a tarball of the snapshot I took in
11/Apr/2006 into a directory named gus-11Apr2006

and the diff between the two is not null:

diff -ruN --exclude=.svn gus-11Apr2006/ gus-23Oct2006/ > gus.diff

In any case, the container helps users just by letting them check
out a GUS environment (gus_home, project_home) ready to be
installed.

I guess that the --revision "{date}" option of svn should
work when checking out the separate modules independently:
GusSchema
install
CBIL
GusAppFramework

Fernan


| Regards,
| 
| Antonio
|
+----]

Re: [GUSDEV] missing prerequisite Error in installation docs

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

Dear Alberto,
The site looks great! Will definitely add a link but was also  
thinking of putting something up on the GUS wiki at http:// 
www.gusdb.org/wiki/ with help from Fernan Aguero and John Iodice.  
Certainly welcome your input as well regarding what makes sense to  
copy, add. just point to or whatever.

Thanks.
Chris

Chris Stoeckert, Ph.D.
Research Professor, Dept. of Genetics
1415 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Ph: 215-573-4409 FAX: 215-573-3111


On Oct 20, 2006, at 3:06 PM, Alberto Davila wrote:

> Hi Chris,
>
> The BiowebDB Consortium has been debugging the postgres version and  
> collecting all the info into:
>
> http://www.biowebdb.org/wiki/index.php/Gus
>
> I am encouraging the students to keep posting all the debugging  
> info there, maybe just copy and/or link the info there for the GUS  
> developers, we would be happy to help with the Postgres version  
> whenever possible ;-)
>
> Cheers, Alberto
>
>
>> ----- Original Message ----- From: "Chris Stoeckert"  
>> <sto...@pc...>
>> To: <an...@ne...>
>> Cc: <gus...@li...>
>> Sent: Friday, October 20, 2006 10:50 AM
>> Subject: Re: [GUSDEV] missing prerequisite Error in installation docs
>>> Sorry that it has been a struggle to get GU-postgres to work and
>>> thanks to all for working out some of the kinks. It would be  
>>> great if
>>> someone could collect the changes that need to be made so that we  
>>> can
>>> correct as needed.
>>>
>>> Thanks,
>>> Chris
>>>
>>> On Oct 20, 2006, at 5:33 AM, an...@ne... wrote:
>>>
>>>> Hello all,
>>>> I've been installing GUS from SVN; installations seems to complete
>>>> without any
>>>> glitch, but 'ga' fails saying that module "Error" is empty.
>>>>
>>>> I solved the issue by installing package Error from CPAN; I think
>>>> this means
>>>> that
>>>> Error should be listed as a prerequisite in the installation docs.
>>>>
>>>> Bye,
>>>>
>>>> Antonio
>>>>
>>>> ----------------------------------------------------------------
>>>> Net Wise webmail system - http://www.netwise.it
>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>
>>>>
>>>> ------------------------------------------------------------------- 
>>>> --- ---
>>>> Using Tomcat but need to do more? Need to support web services,
>>>> security?
>>>> Get stuff done quickly with pre-integrated technology to make your
>>>> job easier
>>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>>> Geronimo
>>>> http://sel.as-us.falkag.net/sel?
>>>> cmd=lnk&kid=120709&bid=263057&dat=121642

Re: [GUSDEV] Fw: missing prerequisite Error in installation docs

[Alberto D. <da...@io...>]

Hi Chris,

The BiowebDB Consortium has been debugging the postgres version and 
collecting all the info into:

http://www.biowebdb.org/wiki/index.php/Gus

I am encouraging the students to keep posting all the debugging info 
there, maybe just copy and/or link the info there for the GUS 
developers, we would be happy to help with the Postgres version whenever 
possible ;-)

Cheers, Alberto


> ----- Original Message ----- From: "Chris Stoeckert" 
> <sto...@pc...>
> To: <an...@ne...>
> Cc: <gus...@li...>
> Sent: Friday, October 20, 2006 10:50 AM
> Subject: Re: [GUSDEV] missing prerequisite Error in installation docs
> 
> 
>> Sorry that it has been a struggle to get GU-postgres to work and
>> thanks to all for working out some of the kinks. It would be great if
>> someone could collect the changes that need to be made so that we can
>> correct as needed.
>>
>> Thanks,
>> Chris
>>
>> On Oct 20, 2006, at 5:33 AM, an...@ne... wrote:
>>
>>> Hello all,
>>> I've been installing GUS from SVN; installations seems to complete
>>> without any
>>> glitch, but 'ga' fails saying that module "Error" is empty.
>>>
>>> I solved the issue by installing package Error from CPAN; I think
>>> this means
>>> that
>>> Error should be listed as a prerequisite in the installation docs.
>>>
>>> Bye,
>>>
>>> Antonio
>>>
>>> ----------------------------------------------------------------
>>> Net Wise webmail system - http://www.netwise.it
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>>
>>> ---------------------------------------------------------------------- 
>>> ---
>>> Using Tomcat but need to do more? Need to support web services,
>>> security?
>>> Get stuff done quickly with pre-integrated technology to make your
>>> job easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>> Geronimo
>>> http://sel.as-us.falkag.net/sel?
>>> cmd=lnk&kid=120709&bid=263057&dat=121642

Re: [GUSDEV] ga +meta --commit

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

michael-

in the ones that had problems, you made a small error.   remove the 
'.pm' from your command line:

no:
 ga +create GUS::Supported::Plugin::LoadRow.pm --commit

yes:

 ga +create GUS::Supported::Plugin::LoadRow --commit


by the way, i'm not sure you need to do this pre-registration step 
anymore in 3.5.    i think the plugin auto-registers the first time you 
use it.

steve

mro...@cs... wrote:

>Steve,
>
>Thanks, it worked, but I got new problems, this is what I did:
>
>found
>at:http://genomics.upenn.edu/~dillo/research/theileria/gus-on-postgres-howto.html
>
>At postgres:
>
>insert into core.databaseversion (
>        database_version_id,
>        version,
>        modification_date,
>        user_read,
>        user_write,
>        group_read,
>        group_write,
>        other_read,
>        other_write,
>        row_user_id,
>        row_group_id,
>        row_project_id,
>        row_alg_invocation_id
>    ) values (
>        nextval('core.databaseversion_sq'),
>        3.5,
>        now(),
>        1, 0, 1, 0, 1, 0,
>        1, 1, 1, 1
>    );
>
>I checked the values in the core.databaseversion table and they are OK
>
>then: ga +meta --commit, and got NO ERRORS
>
>  <Core::Algorithm>
>    <description>GUS application framework for plugins</description>
>    <name>GA-Plugin</name>
>    <Core::AlgorithmImplementation>
>      <executable_md5>f9522ed43f9da502107387a274948971</executable_md5>
>      <executable>GUS::PluginMgr::GusApplication</executable>
>      <cvs_revision>2974</cvs_revision>
>      <Core::AlgorithmInvocation>
>        <result>meta</result>
>        <end_time>now()</end_time>
>        <start_time>now()</start_time>
>        <cpus_used>1</cpus_used>
>      </Core::AlgorithmInvocation>
>    </Core::AlgorithmImplementation>
>  </Core::Algorithm>
>  <Core::Algorithm>
>    <description>GUS application framework for plugins</description>
>    <name>GA-Plugin</name>
>    <modification_date>now()</modification_date>
>    <row_alg_invocation_id>1</row_alg_invocation_id>
>    <row_project_id>1</row_project_id>
>    <row_group_id>1</row_group_id>
>    <row_user_id>1</row_user_id>
>    <other_write>0</other_write>
>    <other_read>1</other_read>
>    <group_write>1</group_write>
>    <group_read>1</group_read>
>    <user_write>1</user_write>
>    <Core::AlgorithmImplementation>
>      <executable_md5>f9522ed43f9da502107387a274948971</executable_md5>
>      <executable>GUS::PluginMgr::GusApplication</executable>
>      <cvs_revision>2974</cvs_revision>
>      <modification_date>now()</modification_date>
>      <row_alg_invocation_id>1</row_alg_invocation_id>
>      <row_project_id>1</row_project_id>
>      <row_group_id>1</row_group_id>
>      <row_user_id>1</row_user_id>
>      <other_write>0</other_write>
>      <other_read>1</other_read>
>      <group_write>1</group_write>
>      <group_read>1</group_read>
>      <user_write>1</user_write>
>      <Core::AlgorithmInvocation>
>        <result>meta</result>
>        <modification_date>now()</modification_date>
>        <end_time>now()</end_time>
>        <start_time>now()</start_time>
>        <row_alg_invocation_id>1</row_alg_invocation_id>
>        <row_project_id>1</row_project_id>
>        <row_group_id>1</row_group_id>
>        <row_user_id>1</row_user_id>
>        <other_write>0</other_write>
>        <other_read>1</other_read>
>        <group_write>1</group_write>
>        <group_read>1</group_read>
>        <user_write>1</user_write>
>        <user_read>1</user_read>
>        <cpus_used>1</cpus_used>
>        <algorithm_implementation_id>2</algorithm_implementation_id>
>        <algorithm_invocation_id>2</algorithm_invocation_id>
>      </Core::AlgorithmInvocation>
>      <user_read>1</user_read>
>      <algorithm_id>2</algorithm_id>
>      <algorithm_implementation_id>2</algorithm_implementation_id>
>    </Core::AlgorithmImplementation>
>    <user_read>1</user_read>
>    <algorithm_id>2</algorithm_id>
>  </Core::Algorithm>
>
>
>I started registering the plugins UNFORTUNATELY I got only 2 correct
>and the next 5 with errors so I stopped to send this email, because maybe
>I need to follow some strict sequence???
>
>  ga +create GUS::Supported::Plugin::LoadTaxon --commit
>  Fri Oct 20 13:06:59 2006        INFO    Plugin
>  GUS::Supported::Plugin::LoadTaxon registered with cvs revision '2943'
>
>  ga +create GUS::Supported::Plugin::InsertExternalDatabase --commit
>  Fri Oct 20 13:13:59 2006        INFO    Plugin
>  GUS::Supported::Plugin::InsertExternalDatabase registered with cvs
>  revision '2942'
>
>ERRORS:
>  ========
>  ga +create GUS::Supported::Plugin::InsertSequenceFeatures.pm --commit
>  Warning: Use of "require" without parens is ambiguous at (eval 8) line 1.
>
>  Bareword "pm" not allowed while "strict subs" in use at (eval 8) line 1.
>  Bareword "GUS::Supported::Plugin::InsertSequenceFeatures" not allowed
>  while "strict subs" in use at (eval 8) line 1.
>  =======
>
>  ga +create GUS::Supported::Plugin::LoadRow.pm --commit
>  Warning: Use of "require" without parens is ambiguous at (eval 8) line 1.
>
>  Bareword "pm" not allowed while "strict subs" in use at (eval 8) line 1.
>  Bareword "GUS::Supported::Plugin::LoadRow" not allowed while "strict
>  subs" in use at (eval 8) line 1.
>  =======
>
>In the meantime I will continue registering the other plugins
>
>Thanks
>
>Michael
>
>
>  
>
>>michael-
>>
>>the 3.5 ga looks in the new table Core.DatabaseVersion in the version
>>column to find out what version of the schema you have.
>>
>>i don't know how that value is supposed to be set, but, you can set it
>>manually to 3.5
>>
>>steve
>>
>>mro...@cs... wrote:
>>
>>    
>>
>>>Hello GUS group,
>>>
>>>I need some help.
>>>
>>>I have been trying to use the ISF plugin in GUS, and to make a long story
>>>short, it appeared that we had a bad GUS 3.5 installed, so we
>>>re-installed, the SVN version of GUS 3.5.
>>>
>>>I am using postgres and the data that was there was erased. Now that I
>>>need to start new, I run the following:
>>>
>>>  ga +meta --commit
>>>
>>>and got:
>>>
>>>  Database version does not match required version for Plugin.
>>>  Database Version:     Plugin Version: 3.5
>>>
>>>
>>>I have looked all over the place in gus...@li...
>>>for an answer but no luck.
>>>
>>>
>>>Your help will be very much appreciated
>>>
>>>
>>>Michael
>>>
>>>
>>>
>>>-------------------------------------------------------------------------
>>>Using Tomcat but need to do more? Need to support web services, security?
>>>Get stuff done quickly with pre-integrated technology to make your job
>>>easier
>>>Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>>Geronimo
>>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>      
>>>
>
>
>
>-------------------------------------------------------------------------
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job easier
>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [GUSDEV] ga +meta --commit

[<mro...@cs...>]

Steve,

Thanks, it worked, but I got new problems, this is what I did:

found
at:http://genomics.upenn.edu/~dillo/research/theileria/gus-on-postgres-ho=
wto.html

At postgres:

insert into core.databaseversion (
        database_version_id,
        version,
        modification_date,
        user_read,
        user_write,
        group_read,
        group_write,
        other_read,
        other_write,
        row_user_id,
        row_group_id,
        row_project_id,
        row_alg_invocation_id
    ) values (
        nextval('core.databaseversion_sq'),
        3.5,
        now(),
        1, 0, 1, 0, 1, 0,
        1, 1, 1, 1
    );

I checked the values in the core.databaseversion table and they are OK

then: ga +meta --commit, and got NO ERRORS

  <Core::Algorithm>
    <description>GUS application framework for plugins</description>
    <name>GA-Plugin</name>
    <Core::AlgorithmImplementation>
      <executable_md5>f9522ed43f9da502107387a274948971</executable_md5>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <cvs_revision>2974</cvs_revision>
      <Core::AlgorithmInvocation>
        <result>meta</result>
        <end_time>now()</end_time>
        <start_time>now()</start_time>
        <cpus_used>1</cpus_used>
      </Core::AlgorithmInvocation>
    </Core::AlgorithmImplementation>
  </Core::Algorithm>
  <Core::Algorithm>
    <description>GUS application framework for plugins</description>
    <name>GA-Plugin</name>
    <modification_date>now()</modification_date>
    <row_alg_invocation_id>1</row_alg_invocation_id>
    <row_project_id>1</row_project_id>
    <row_group_id>1</row_group_id>
    <row_user_id>1</row_user_id>
    <other_write>0</other_write>
    <other_read>1</other_read>
    <group_write>1</group_write>
    <group_read>1</group_read>
    <user_write>1</user_write>
    <Core::AlgorithmImplementation>
      <executable_md5>f9522ed43f9da502107387a274948971</executable_md5>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <cvs_revision>2974</cvs_revision>
      <modification_date>now()</modification_date>
      <row_alg_invocation_id>1</row_alg_invocation_id>
      <row_project_id>1</row_project_id>
      <row_group_id>1</row_group_id>
      <row_user_id>1</row_user_id>
      <other_write>0</other_write>
      <other_read>1</other_read>
      <group_write>1</group_write>
      <group_read>1</group_read>
      <user_write>1</user_write>
      <Core::AlgorithmInvocation>
        <result>meta</result>
        <modification_date>now()</modification_date>
        <end_time>now()</end_time>
        <start_time>now()</start_time>
        <row_alg_invocation_id>1</row_alg_invocation_id>
        <row_project_id>1</row_project_id>
        <row_group_id>1</row_group_id>
        <row_user_id>1</row_user_id>
        <other_write>0</other_write>
        <other_read>1</other_read>
        <group_write>1</group_write>
        <group_read>1</group_read>
        <user_write>1</user_write>
        <user_read>1</user_read>
        <cpus_used>1</cpus_used>
        <algorithm_implementation_id>2</algorithm_implementation_id>
        <algorithm_invocation_id>2</algorithm_invocation_id>
      </Core::AlgorithmInvocation>
      <user_read>1</user_read>
      <algorithm_id>2</algorithm_id>
      <algorithm_implementation_id>2</algorithm_implementation_id>
    </Core::AlgorithmImplementation>
    <user_read>1</user_read>
    <algorithm_id>2</algorithm_id>
  </Core::Algorithm>


I started registering the plugins UNFORTUNATELY I got only 2 correct
and the next 5 with errors so I stopped to send this email, because maybe
I need to follow some strict sequence???

  ga +create GUS::Supported::Plugin::LoadTaxon --commit
  Fri Oct 20 13:06:59 2006        INFO    Plugin
  GUS::Supported::Plugin::LoadTaxon registered with cvs revision '2943'

  ga +create GUS::Supported::Plugin::InsertExternalDatabase --commit
  Fri Oct 20 13:13:59 2006        INFO    Plugin
  GUS::Supported::Plugin::InsertExternalDatabase registered with cvs
  revision '2942'

ERRORS:
  =3D=3D=3D=3D=3D=3D=3D=3D
  ga +create GUS::Supported::Plugin::InsertSequenceFeatures.pm --commit
  Warning: Use of "require" without parens is ambiguous at (eval 8) line =
1.

  Bareword "pm" not allowed while "strict subs" in use at (eval 8) line 1=
.
  Bareword "GUS::Supported::Plugin::InsertSequenceFeatures" not allowed
  while "strict subs" in use at (eval 8) line 1.
  =3D=3D=3D=3D=3D=3D=3D

  ga +create GUS::Supported::Plugin::LoadRow.pm --commit
  Warning: Use of "require" without parens is ambiguous at (eval 8) line =
1.

  Bareword "pm" not allowed while "strict subs" in use at (eval 8) line 1=
.
  Bareword "GUS::Supported::Plugin::LoadRow" not allowed while "strict
  subs" in use at (eval 8) line 1.
  =3D=3D=3D=3D=3D=3D=3D

In the meantime I will continue registering the other plugins

Thanks

Michael


> michael-
>
> the 3.5 ga looks in the new table Core.DatabaseVersion in the version
> column to find out what version of the schema you have.
>
> i don't know how that value is supposed to be set, but, you can set it
> manually to 3.5
>
> steve
>
> mro...@cs... wrote:
>
>>Hello GUS group,
>>
>>I need some help.
>>
>>I have been trying to use the ISF plugin in GUS, and to make a long sto=
ry
>>short, it appeared that we had a bad GUS 3.5 installed, so we
>>re-installed, the SVN version of GUS 3.5.
>>
>>I am using postgres and the data that was there was erased. Now that I
>>need to start new, I run the following:
>>
>>   ga +meta --commit
>>
>>and got:
>>
>>   Database version does not match required version for Plugin.
>>   Database Version:     Plugin Version: 3.5
>>
>>
>>I have looked all over the place in gus...@li...
>>for an answer but no luck.
>>
>>
>>Your help will be very much appreciated
>>
>>
>>Michael
>>
>>
>>
>>-----------------------------------------------------------------------=
--
>>Using Tomcat but need to do more? Need to support web services, securit=
y?
>>Get stuff done quickly with pre-integrated technology to make your job
>> easier
>>Download IBM WebSphere Application Server v.1.0.1 based on Apache
>> Geronimo
>>http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>

Re: [GUSDEV] missing prerequisite Error in installation docs

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

Sorry that it has been a struggle to get GU-postgres to work and  
thanks to all for working out some of the kinks. It would be great if  
someone could collect the changes that need to be made so that we can  
correct as needed.

Thanks,
Chris

On Oct 20, 2006, at 5:33 AM, an...@ne... wrote:

> Hello all,
> I've been installing GUS from SVN; installations seems to complete  
> without any
> glitch, but 'ga' fails saying that module "Error" is empty.
>
> I solved the issue by installing package Error from CPAN; I think  
> this means
> that
> Error should be listed as a prerequisite in the installation docs.
>
> Bye,
>
> Antonio
>
> ----------------------------------------------------------------
> Net Wise webmail system - http://www.netwise.it
> This message was sent using IMP, the Internet Messaging Program.
>
>
> ---------------------------------------------------------------------- 
> ---
> Using Tomcat but need to do more? Need to support web services,  
> security?
> Get stuff done quickly with pre-integrated technology to make your  
> job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache  
> Geronimo
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] ga +meta --commit

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

michael-

the 3.5 ga looks in the new table Core.DatabaseVersion in the version 
column to find out what version of the schema you have.

i don't know how that value is supposed to be set, but, you can set it 
manually to 3.5

steve

mro...@cs... wrote:

>Hello GUS group,
>
>I need some help.
>
>I have been trying to use the ISF plugin in GUS, and to make a long story
>short, it appeared that we had a bad GUS 3.5 installed, so we
>re-installed, the SVN version of GUS 3.5.
>
>I am using postgres and the data that was there was erased. Now that I
>need to start new, I run the following:
>
>   ga +meta --commit
>
>and got:
>
>   Database version does not match required version for Plugin.
>   Database Version:     Plugin Version: 3.5
>
>
>I have looked all over the place in gus...@li...
>for an answer but no luck.
>
>
>Your help will be very much appreciated
>
>
>Michael
>
>
>
>-------------------------------------------------------------------------
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job easier
>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[GUSDEV] ga +meta --commit

[<mro...@cs...>]

Hello GUS group,

I need some help.

I have been trying to use the ISF plugin in GUS, and to make a long story
short, it appeared that we had a bad GUS 3.5 installed, so we
re-installed, the SVN version of GUS 3.5.

I am using postgres and the data that was there was erased. Now that I
need to start new, I run the following:

   ga +meta --commit

and got:

   Database version does not match required version for Plugin.
   Database Version:     Plugin Version: 3.5


I have looked all over the place in gus...@li...
for an answer but no luck.


Your help will be very much appreciated


Michael

[GUSDEV] missing prerequisite Error in installation docs

[<an...@ne...>]

Hello all,
I've been installing GUS from SVN; installations seems to complete withou=
t any
glitch, but 'ga' fails saying that module "Error" is empty.

I solved the issue by installing package Error from CPAN; I think this me=
ans
that
Error should be listed as a prerequisite in the installation docs.

Bye,

Antonio

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Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[<an...@ne...>]

Quoting Fernan Aguero <fe...@ii...>:

> So I'd say that you're safe using the trunk ... at least
> until 3.6 comes out (because then the 3.6 branch will be
> merged to trunk, correct?. At least this is how I now understand it.
> Others please correct me if I'm wrong).

I've been re-reading the install documentation, and that's what made us t=
ake
the decision of avoiding SVN in the first place:

  Warning

  Since the 3.5 release of GUS, the source repository is no longer the
  preferred or recommended method for downloading GUS. The source reposit=
ory
  contains the most recent additions and changes to GUS, which may be
  inconsistent with this and other documentation, and which may include c=
hanged
  APIs that could cause data loss.

If this information no longer applies, that's probably a part that should=
 be
corrected, isn't it?

> But in any case you can always checkout a snapshot from any point back =
in
> time...

I've tried to, but just don't seem to be able to: gusTrunk is an empty
container that relies on other external trunks for getting the real softw=
are.
No matter what release I ask for, I always end up with the latest tree be=
ing
checked out for these external sources. For instance, the command

svn co --revision {2006-04-11} https://www.cbil.upenn.edu/svn/gus/gusTrun=
k .

terminates with the following lines:

------------------------------------------------------
Fetching external item into 'project_home/install'
 ...
Checked out external at revision 5069.


Fetching external item into 'project_home/GusSchema'
 ...
Checked out external at revision 5069.

Checked out revision 4752.
------------------------------------------------------

Regards,

Antonio




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Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[Fernan A. <fe...@ii...>]

+----[ an...@ne... <an...@ne...> (17.Oct.2006 13:29):
|
| Quoting Fernan Aguero <fe...@ii...>:
| 
| > After 3.5 there are many bugfixes, but no release tarball.
| > Most of us are working off the svn repository. Not having a
| > release tarball to go back to might make you feel
| > uncomfortable
| 
| Yes, that's why we choose the release tarball. Most of the software I have
| been using from SVN is usually untested and far from production quality.
| It seems that with GUS it's best to live on the bleeding edge instead: well,
| that's good to know, so thanks for telling me :)

in GUS the trunk is not the bleeding edge. The bleeding edge
lives in the branches (for example the '3.6-Dev' branch of
the GusSchema).

I also had the same idea about software coming from version
control repositories ... mostly based on the projects I knew
at the time: a moving (unstable) trunk with one or more
'stable' branches. But, it seems like in GUS the development
model is different: a stable trunk with one or more
'unstable' development branches. After knowing this, I've
now come across many other projects using this model, so
it's not only GUS that's using it.

So I'd say that you're safe using the trunk ... at least
until 3.6 comes out (because then the 3.6 branch will be
merged to trunk, correct?. At least this is how I now understand it.
Others please correct me if I'm wrong). But in any case you
can always checkout a snapshot from any point back in time
... 

Fernan
 
| > perhaps the upgrade.txt instructions in
| > project_home/GusSchema/Definition/config/?
| >
| > I've never done this upgrade. Perhaps there are other
| > upgrade instructions to follow ...
| 
| I'll take a look, but probably I'd better start again from scratch; at least
| I will be sure about which version I have.
|
| Thanks again,
| 
| Antonio
|
+----]

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[<an...@ne...>]

Quoting Fernan Aguero <fe...@ii...>:

> After 3.5 there are many bugfixes, but no release tarball.
> Most of us are working off the svn repository. Not having a
> release tarball to go back to might make you feel
> uncomfortable

Yes, that's why we choose the release tarball. Most of the software I hav=
e
been using from SVN is usually untested and far from production quality.
It seems that with GUS it's best to live on the bleeding edge instead: we=
ll,
that's good to know, so thanks for telling me :)

> perhaps the upgrade.txt instructions in
> project_home/GusSchema/Definition/config/?
>
> I've never done this upgrade. Perhaps there are other
> upgrade instructions to follow ...

I'll take a look, but probably I'd better start again from scratch; at le=
ast
I will be sure about which version I have.

Thanks again,

Antonio







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Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[Fernan A. <fe...@ii...>]

+----[ an...@ne... <an...@ne...> (17.Oct.2006 11:40):
|
| Quoting Fernan Aguero <fe...@ii...>:
| 
| > we're using PostgreSQL with GUS 3.5.1 over here and we've
| > not seen this error while using the supported ISF plugin.
| 
| Hi Fernan,
| thanks a lot for your feedback.
| 
| The views you show are clearly ok, so after your mail I had a look at the file
| GusClassHierarchyConverter.java in SVN, and the code there is in fact already
| fixed.

Good to know :)

| We originally chose version 3.5.0.0 since, according to the download page on
| www.gusdb.org, it was the latest official release (it still is, for that
| matter).

Yes the download page mentions that 3.5 is the latest stable
release. But IMO the page should be updated. I guess that
the meaning of this notice is to say that 3.5 is the latest
stable release that can be downloaded as a release tarball.

After 3.5 there are many bugfixes, but no release tarball.
Most of us are working off the svn repository. Not having a
release tarball to go back to might make you feel
uncomfortable, but in fact, if you ever want to get an exact
same snapshot of something you checked out of the repository
you just have to:

i) take note of the revision you're checking out
or 
ii) take note of the date of the checkout

In our case, we checked out everything from the repository
on 11th April, 2006. So in case we want to to reproduce
exactly what we've done, we could just do:

svn checkout --revision {2006-04-11}

| John, is there any smooth upgrade path to jump up to the version that Fernan
| has? I hope I won't need to rebuild everything from scratch...

perhaps the upgrade.txt instructions in 
project_home/GusSchema/Definition/config/?

I've never done this upgrade. Perhaps there are other
upgrade instructions to follow ... 

Fernan

| Antonio
|
+----]

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[<an...@ne...>]

Quoting Fernan Aguero <fe...@ii...>:

> we're using PostgreSQL with GUS 3.5.1 over here and we've
> not seen this error while using the supported ISF plugin.

Hi Fernan,
thanks a lot for your feedback.

The views you show are clearly ok, so after your mail I had a look at the=
 file
GusClassHierarchyConverter.java in SVN, and the code there is in fact alr=
eady
fixed.

We originally chose version 3.5.0.0 since, according to the download page=
 on
www.gusdb.org, it was the latest official release (it still is, for that
matter).

John, is there any smooth upgrade path to jump up to the version that Fer=
nan
has? I hope I won't need to rebuild everything from scratch...

Antonio


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Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[Fernan A. <fe...@ii...>]

+----[ an...@ne... <an...@ne...> (17.Oct.2006 05:57):
|
| Quoting John Iodice <io...@pc...>:
|=20
| > Can you tell me more about what was happening when the error occurred?
|=20
| The command I was running is the following:
|=20
| ga GUS::Supported::Plugin::InsertSequenceFeatures
|    --mapFile /hardmnt/mpa/gus/GUS/gus_home/config/genbank2gus.xml
|    --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank
|    --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16
|    --veryVerbose --sqlVerbose
|    --commit
|=20
| The error, occurring at the end of the import run, is this one:
|=20
| sqlExec:
|  INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from DoTS.Source v
|  where v.na_feature_id =3D ?
|  bindValues (5)
|=20
| DBD::Pg::st execute failed: ERROR:  null value in column "na_feature_id"
| violates not-null constraint at
| /hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 14=
7,
| <GEN39> line 368238.
|=20
| The script does import the data anyway, leaving me to wonder if there is =
no
| transaction support (or if it is broken).

Antonio and John,

we're using PostgreSQL with GUS 3.5.1 over here and we've
not seen this error while using the supported ISF plugin.

and I don't remember doing anything weird to our
installation (patching and/or editing).

| > Mike mentioned the install logs; do you still have those?  If so,
| > please send me a copy.
|=20
| I haven't got the schema building logs any more, but I attach you the
| objects.sql that produced my schema - as you can see, it is already wrong=
 at
| this level: all of the versioned views have incomplete rules for insert a=
nd
| update.
|
| > There are some other people using GUS and PostgreSQL.  Do you know
| > why they haven't encountered the error (or how they worked around it)?
|
+----]

[rest of message snipped]

We're one of those. And AFAIR we haven't done anything
special on our installation. I don't remember coming across
this error, but other than that, how can we tell if our
schema is right or if we lack rules for insert/update? I
mean at the psql level ... is this related only to the
dotsver.sourcever table or are more tables involved (see at
the end of this message the information for the
dotsver.sourcever table I got from psql).

Fernan

PS: output of '\d dotsver.sourcever'


                        View "dotsver.sourcever"
            Column            |            Type             | Modifiers=20
------------------------------+-----------------------------+-----------
 na_feature_id                | numeric(10,0)               |=20
 na_sequence_id               | numeric(10,0)               |=20
 subclass_view                | character varying(30)       |=20
 name                         | character varying(30)       |=20
 sequence_ontology_id         | numeric(10,0)               |=20
 parent_id                    | numeric(10,0)               |=20
 external_database_release_id | numeric(10,0)               |=20
 source_id                    | character varying(50)       |=20
 prediction_algorithm_id      | numeric(5,0)                |=20
 is_predicted                 | numeric(1,0)                |=20
 review_status_id             | numeric(10,0)               |=20
 cell_line                    | character varying(4000)     |=20
 cell_type                    | character varying(4000)     |=20
 chromoplast                  | character varying(4000)     |=20
 chromosome                   | character varying(4000)     |=20
 clone                        | character varying(4000)     |=20
 clone_lib                    | character varying(4000)     |=20
 cultivar                     | character varying(4000)     |=20
 cyanelle                     | character varying(4000)     |=20
 dev_stage                    | character varying(4000)     |=20
 focus                        | character varying(4000)     |=20
 frequency                    | character varying(4000)     |=20
 germline                     | character varying(4000)     |=20
 haplotype                    | character varying(4000)     |=20
 insertion_seq                | text                        |=20
 isolate                      | character varying(4000)     |=20
 kinetoplast                  | character varying(4000)     |=20
 lab_host                     | character varying(4000)     |=20
 macronuclear                 | character varying(4000)     |=20
 organelle                    | character varying(4000)     |=20
 pop_variant                  | character varying(4000)     |=20
 plasmid                      | character varying(4000)     |=20
 proviral                     | character varying(4000)     |=20
 rearranged                   | character varying(4000)     |=20
 sequenced_mol                | character varying(4000)     |=20
 serotype                     | character varying(4000)     |=20
 sex                          | character varying(4000)     |=20
 specific_host                | character varying(4000)     |=20
 strain                       | character varying(4000)     |=20
 sub_clone                    | character varying(4000)     |=20
 sub_species                  | character varying(4000)     |=20
 sub_strain                   | character varying(4000)     |=20
 tissue_lib                   | character varying(4000)     |=20
 transposon                   | character varying(4000)     |=20
 variety                      | character varying(4000)     |=20
 virion                       | character varying(4000)     |=20
 chloroplast                  | character varying(4000)     |=20
 citation                     | character varying(4000)     |=20
 map                          | character varying(4000)     |=20
 organism                     | character varying(4000)     |=20
 specimen_voucher             | character varying(4000)     |=20
 tissue_type                  | character varying(4000)     |=20
 usedin                       | character varying(4000)     |=20
 label                        | character varying(4000)     |=20
 modification_date            | timestamp without time zone |=20
 user_read                    | numeric(1,0)                |=20
 user_write                   | numeric(1,0)                |=20
 group_read                   | numeric(1,0)                |=20
 group_write                  | numeric(1,0)                |=20
 other_read                   | numeric(1,0)                |=20
 other_write                  | numeric(1,0)                |=20
 row_user_id                  | numeric(12,0)               |=20
 row_group_id                 | numeric(4,0)                |=20
 row_project_id               | numeric(4,0)                |=20
 row_alg_invocation_id        | numeric(12,0)               |=20
 version_alg_invocation_id    | numeric(12,0)               |=20
 version_date                 | timestamp without time zone |=20
 version_transaction_id       | numeric(12,0)               |=20
View definition:
 SELECT nafeatureimpver.na_feature_id, nafeatureimpver.na_sequence_id, nafe=
atureimpver.subclass_view, nafeatureimpver.name, nafeatureimpver.sequence_o=
ntology_id, nafeatureimpver.parent_id, nafeatureimpver.external_database_re=
lease_id, nafeatureimpver.source_id, nafeatureimpver.prediction_algorithm_i=
d, nafeatureimpver.is_predicted, nafeatureimpver.review_status_id, nafeatur=
eimpver.string1 AS cell_line, nafeatureimpver.string2 AS cell_type, nafeatu=
reimpver.string3 AS chromoplast, nafeatureimpver.string4 AS chromosome, naf=
eatureimpver.string5 AS clone, nafeatureimpver.string6 AS clone_lib, nafeat=
ureimpver.string7 AS cultivar, nafeatureimpver.string8 AS cyanelle, nafeatu=
reimpver.string9 AS dev_stage, nafeatureimpver.string10 AS focus, nafeature=
impver.string11 AS frequency, nafeatureimpver.string12 AS germline, nafeatu=
reimpver.string13 AS haplotype, nafeatureimpver.clob1 AS insertion_seq, naf=
eatureimpver.string14 AS isolate, nafeatureimpver.string15 AS kinetoplast, =
nafeatureimpver.string16 AS lab_host, nafeatureimpver.string17 AS macronucl=
ear, nafeatureimpver.string18 AS organelle, nafeatureimpver.string19 AS pop=
_variant, nafeatureimpver.string20 AS plasmid, nafeatureimpver.string21 AS =
proviral, nafeatureimpver.string22 AS rearranged, nafeatureimpver.string23 =
AS sequenced_mol, nafeatureimpver.string24 AS serotype, nafeatureimpver.str=
ing25 AS sex, nafeatureimpver.string26 AS specific_host, nafeatureimpver.st=
ring27 AS strain, nafeatureimpver.string28 AS sub_clone, nafeatureimpver.st=
ring29 AS sub_species, nafeatureimpver.string30 AS sub_strain, nafeatureimp=
ver.string31 AS tissue_lib, nafeatureimpver.string32 AS transposon, nafeatu=
reimpver.string33 AS variety, nafeatureimpver.string34 AS virion, nafeature=
impver.string35 AS chloroplast, nafeatureimpver.string36 AS citation, nafea=
tureimpver.string37 AS map, nafeatureimpver.string38 AS organism, nafeature=
impver.string39 AS specimen_voucher, nafeatureimpver.string40 AS tissue_typ=
e, nafeatureimpver.string41 AS usedin, nafeatureimpver.string42 AS label, n=
afeatureimpver.modification_date, nafeatureimpver.user_read, nafeatureimpve=
r.user_write, nafeatureimpver.group_read, nafeatureimpver.group_write, nafe=
atureimpver.other_read, nafeatureimpver.other_write, nafeatureimpver.row_us=
er_id, nafeatureimpver.row_group_id, nafeatureimpver.row_project_id, nafeat=
ureimpver.row_alg_invocation_id, nafeatureimpver.version_alg_invocation_id,=
 nafeatureimpver.version_date, nafeatureimpver.version_transaction_id
   FROM dotsver.nafeatureimpver
  WHERE nafeatureimpver.subclass_view::text =3D 'Source'::text;
Rules:
 sourcever_72791 AS
    ON INSERT TO dotsver.sourcever DO INSTEAD  INSERT INTO dotsver.nafeatur=
eimpver (na_feature_id, na_sequence_id, subclass_view, name, sequence_ontol=
ogy_id, parent_id, external_database_release_id, source_id, prediction_algo=
rithm_id, is_predicted, review_status_id, string1, string2, string3, string=
4, string5, string6, string7, string8, string9, string10, string11, string1=
2, string13, clob1, string14, string15, string16, string17, string18, strin=
g19, string20, string21, string22, string23, string24, string25, string26, =
string27, string28, string29, string30, string31, string32, string33, strin=
g34, string35, string36, string37, string38, string39, string40, string41, =
string42, modification_date, user_read, user_write, group_read, group_write=
, other_read, other_write, row_user_id, row_group_id, row_project_id, row_a=
lg_invocation_id, version_alg_invocation_id, version_date, version_transact=
ion_id)=20
  VALUES (new.na_feature_id, new.na_sequence_id, new.subclass_view, new.nam=
e, new.sequence_ontology_id, new.parent_id, new.external_database_release_i=
d, new.source_id, new.prediction_algorithm_id, new.is_predicted, new.review=
_status_id, new.cell_line, new.cell_type, new.chromoplast, new.chromosome, =
new.clone, new.clone_lib, new.cultivar, new.cyanelle, new.dev_stage, new.fo=
cus, new.frequency, new.germline, new.haplotype, new.insertion_seq, new.iso=
late, new.kinetoplast, new.lab_host, new.macronuclear, new.organelle, new.p=
op_variant, new.plasmid, new.proviral, new.rearranged, new.sequenced_mol, n=
ew.serotype, new.sex, new.specific_host, new.strain, new.sub_clone, new.sub=
_species, new.sub_strain, new.tissue_lib, new.transposon, new.variety, new.=
virion, new.chloroplast, new.citation, new.map, new.organism, new.specimen_=
voucher, new.tissue_type, new.usedin, new.label, new.modification_date, new=
=2Euser_read, new.user_write, new.group_read, new.group_write, new.other_re=
ad, new.other_write, new.row_user_id, new.row_group_id, new.row_project_id,=
 new.row_alg_invocation_id, new.version_alg_invocation_id, new.version_date=
, new.version_transaction_id)

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[<an...@ne...>]

Quoting John Iodice <io...@pc...>:

> Can you tell me more about what was happening when the error occurred?

The command I was running is the following:

ga GUS::Supported::Plugin::InsertSequenceFeatures
   --mapFile /hardmnt/mpa/gus/GUS/gus_home/config/genbank2gus.xml
   --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank
   --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16
   --veryVerbose --sqlVerbose
   --commit

The error, occurring at the end of the import run, is this one:

sqlExec:
 INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from DoTS.Source v
 where v.na_feature_id =3D ?
 bindValues (5)

DBD::Pg::st execute failed: ERROR:  null value in column "na_feature_id"
violates not-null constraint at
/hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 14=
7,
<GEN39> line 368238.

The script does import the data anyway, leaving me to wonder if there is =
no
transaction support (or if it is broken).

> Mike mentioned the install logs; do you still have those?  If so,
> please send me a copy.

I haven't got the schema building logs any more, but I attach you the
objects.sql that produced my schema - as you can see, it is already wrong=
 at
this level: all of the versioned views have incomplete rules for insert a=
nd
update.

> There are some other people using GUS and PostgreSQL.  Do you know
> why they haven't encountered the error (or how they worked around it)?

I'd say that most people just wouldn't bother to report it, since the dat=
a
gets inserted anyway.

> Even if it isn't a problem for my project, I'll help if I can; part
> of my job is to contribute to the development of PostgreSQL GUS, so
> I'd like to see this fixed.  Email me (or the group) with any
> progress you make, and I'll do the same.

I fear I have been too cryptic in my previous mail, since you seem to sta=
rt
this bug-hunting from the very beginning: I did find the root cause for i=
t,
and actually tried to communicate it to the list... so bear with me, and =
let
me try again.

The problem is that the versioned views on subclasses are generated
incorrectly; specifically, they miss the base (inherited) columns. This
inconsistency in the definition generates the wrong ON INSERT/ON UPDATE
rules on PostgreSQL.

Now, let me try to express this point in more detail.

So, let's start from the file

 GUS/Schema/src/java/org/gusdb/schema/InstallSchemaTask.java

which is responsible for creating the objects.sql script. Looking at func=
tion
execute(), at line 93 you find the instruction

   convertSubclasses( db );

that generates the database implementation for subclasses: for each class
which subclasses, it calls GusClassHierarchyConverter like this (same fil=
e,
line 143):

   for ( Iterator i =3D superClasses.iterator(); i.hasNext();  ) {
     GusClassHierarchyConverter converter =3D
         new GusClassHierarchyConverter( (GusTable) i.next() );
     converter.convert();
   }

Now, this code snipped is responsible for generating the base table and a=
ll
the views needed to implement the class/subclass hierarchy.

Now, the problem is that

 GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.j=
ava

is incorrectly handling this generation task when it comes to subclasses =
of
version views.

Let's dissect this point a bit further, then: have a look at the converte=
r
code, specifically at function buildSuperClassView() (line 417 in GUS 3.5=
)
and function buildSubClassView() (line 510).

If the implementation table is versioned, then it should create a version=
 also
for the superClassView. Now, the code does generate the correct SQL state=
ment
for creating the version view, but does not add all of the columns to the=
 Java
object.

The following snippet (line 444, same file) is very clear:

  if (impTable.isVersioned()) {
    superClassView.setVersioned(true);
    verSql =3D sql.concat(" ");
    for (Iterator i =3D verHousekeepingColumns.iterator(); i.hasNext();) =
{
      Column column =3D (Column)i.next();
      verSql =3D verSql.concat(", " + column.getName());
      superClassView.getVersionView().addColumn(new
        ColumnPair(column.getName(), column.getName()));
    }
    verSql =3D verSql.concat(
      " FROM " +
      impTable.getVersionTable().getSchema().getName() +
      "." + impTable.getVersionTable().getName() +
      ";");
    superClassView.getVersionView().setSql(verSql);
  }

As you can see, the Java object superClassView.getVersionView() is explic=
itly
added all of the verHousekeepingColums, but there is no code _here_ that =
puts
the original columns of superClassView into its versioned view.

So, one might expect that this task (ie, copying all of the base columns =
into
the versioned view) is accomplished by the statement

    superClassView.setVersioned(true);

(which is in fact the behaviour of method setVersioned(true) in GusTable)=
.

Unluckily, the code for method setVersioned() in file

  GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/GusView.java

is the following:

    public void setVersioned(boolean versioned) {
        if ( this.versioned && ! versioned ) {
            this.versioned =3D versioned;
            this.versionView.setSchema(null);
            this.versionView =3D null;
        }
        if ( ! this.versioned && versioned ) {
            this.versioned =3D versioned;
            versionView =3D new VersionView(this);
        }
    }

so as you can see, the colums appearing in GusView are NOT copied to its
versioned view.

Getting back to the original point, ie is the creation of the schema: the
installer

 GUS/Schema/src/java/org/gusdb/schema/InstallSchemaTask.java

is now working with the incompletely populated versioned views. In my cas=
e,
the installer hands the class hyerarchy to

 GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java

which uses (line 133)

    protected void writeView(View view) throws IOException {
        super.writeView(view);
        writeViewRules(view);
    }

to create the SQL statements for each view. Now, writeViewRules makes use=
 of
the columns stored inside views to create the RULES (see line 146).

I've also had a look at the Oracle side: in that case, the writeView() me=
thod
is inherited from

 GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/RelationalDatabaseWriter.j=
ava

and does use the versioned views columns at all, so Oracle installations =
won't
be affected by this bug - not during the schema generation, at least.

I sincerely hope that this email is a tad clearer than the previous one; =
but
please let me know if I can help on this matter further.

Bye,

Antonio



----------------------------------------------------------------
Net Wise webmail system - http://www.netwise.it
This message was sent using IMP, the Internet Messaging Program.

Re: [GUSDEV] dba scripts

[Michael S. <m...@sa...>]

Hi Mark,

Sorry for the confusion.  It stems from the fact that there are really two =
pieces of GUS-- the application framework and the schema.  In general, the =
must correspond (i.e. The schema 3.5 goes with the 3.5 app framework).  In =
this case, however, the dbaDumpSchema script is (or should be if memory ser=
ves me correctly) schema independent but it does require the 3.5 app framew=
ork. =20

So, your understanding below is correct.

--Mike

--
Sent from Windows Mobile.
-----Original Message-----
From: marc jackson <de...@ho...>
Sent: Monday, October 16, 2006 4:48 PM
To: m...@sa...; gus...@li...
Subject: Re: [GUSDEV] dba scripts


Hi Michael.

I'm a little confused.  I thought that I needed to dump the schema from 3.0=
=20
and re-import it
into 3.5.*.   I thought that using the dba scripts would be the methodology=
=20
for the export/import.

If I understood you correctly, you're saying:

1. install 3.5.1 in a different place, ignoring the DB portion.
2. use the 3.5.1 dba scripts to dump/restore the schema's.

Is that correct?

Regards,

Marc

>From: "Michael Saffitz" <m...@sa...>
>To: "marc jackson"=20
><de...@ho...>,<gus...@li...>
>Subject: Re: [GUSDEV] dba scripts
>Date: Mon, 16 Oct 2006 15:45:38 -0700
>
>
>Hi Marc,
>
>Ok,  I'd recommend getting 3.5.1 (or whatever the latest is), installing=20
>the app framework in a new location (just skip the step on installing the=
=20
>DB), and then using the dbaDumpSchema script.
>
>3.0 is pretty old, and I'm not sure the extent that those admin scripts=20
>(i.e. dumpSchema) still work.
>
>--Mike
>
>----- Original Message ----- From: "marc jackson" <de...@ho...>
>To: <m...@sa...>; <gus...@li...>
>Sent: Monday, October 16, 2006 3:36 PM
>Subject: Re: [GUSDEV] dba scripts
>
>
>>Hi Michael,
>>
>>re: dba scripts. We exchanged emails earlier. I know that I need to dump=
=20
>>the schema from the
>>database before I do an upgrade on GUS.  I'm trying to use the script:=20
>>dumpSchema.pl.
>>Essentially, the dba admin scripts need to be rebuilt to utilize the perl=
=20
>>that's on this system.
>>
>>We're using code 3.0.  I can't find the old code anywhere.
>>
>>Regards,
>>
>>Marc
>>
>>
>>
>>
>>>From: "Michael Saffitz" <m...@sa...>
>>>To: "marc jackson"=20
>>><de...@ho...>,<gus...@li...>
>>>Subject: Re: [GUSDEV] dba scripts
>>>Date: Mon, 16 Oct 2006 12:16:59 -0700
>>>
>>>
>>>Hi Marc,
>>>
>>>I think more information is needed here:
>>>
>>>1) Which dba scripts are you attempting to use?  What is occuring that=20
>>>leads you to believe they are not working (i.e. can you paste the error=
=20
>>>you're seeing?)
>>>
>>>2) What code base do you have at the moment? 3.0, 3.5?  I assume your DB=
=20
>>>is 3.0, and you want to upgrade it to 3.5?  This is non-trivial, and you=
=20
>>>should search the list archives for more information about general steps=
=20
>>>and advice.
>>>
>>>--Mike
>>>
>>>----- Original Message ----- From: "marc jackson" <de...@ho...>
>>>To: <gus...@li...>
>>>Sent: Monday, October 16, 2006 6:37 AM
>>>Subject: [GUSDEV] dba scripts
>>>
>>>
>>>>Hello,
>>>>
>>>>I'm trying to do an upgrade from 3.0 to 3.5.
>>>>The dba scripts don't work [ possibly due to
>>>>a hard disk failure/faulty restore ]. Does
>>>>anyone know how to rebuid/recompile the
>>>>dba scripts.
>>>>
>>>>I ran build GUS -append, but this had no
>>>>effect.  I also re-installed Oracle 10.
>>>>
>>>>Regards,
>>>>
>>>>Marc
>>>>
>>>>
>>>>
>>>>-----------------------------------------------------------------------=
--
>>>>Using Tomcat but need to do more? Need to support web services,=20
>>>>security?
>>>>Get stuff done quickly with pre-integrated technology to make your job=
=20
>>>>easier
>>>>Download IBM WebSphere Application Server v.1.0.1 based on Apache=20
>>>>Geronimo
>>>>http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>
>>
>>
>>
>

Re: [GUSDEV] dba scripts

[marc j. <de...@ho...>]

Hi Michael.

I'm a little confused.  I thought that I needed to dump the schema from 3.0 
and re-import it
into 3.5.*.   I thought that using the dba scripts would be the methodology 
for the export/import.

If I understood you correctly, you're saying:

1. install 3.5.1 in a different place, ignoring the DB portion.
2. use the 3.5.1 dba scripts to dump/restore the schema's.

Is that correct?

Regards,

Marc

>From: "Michael Saffitz" <m...@sa...>
>To: "marc jackson" 
><de...@ho...>,<gus...@li...>
>Subject: Re: [GUSDEV] dba scripts
>Date: Mon, 16 Oct 2006 15:45:38 -0700
>
>
>Hi Marc,
>
>Ok,  I'd recommend getting 3.5.1 (or whatever the latest is), installing 
>the app framework in a new location (just skip the step on installing the 
>DB), and then using the dbaDumpSchema script.
>
>3.0 is pretty old, and I'm not sure the extent that those admin scripts 
>(i.e. dumpSchema) still work.
>
>--Mike
>
>----- Original Message ----- From: "marc jackson" <de...@ho...>
>To: <m...@sa...>; <gus...@li...>
>Sent: Monday, October 16, 2006 3:36 PM
>Subject: Re: [GUSDEV] dba scripts
>
>
>>Hi Michael,
>>
>>re: dba scripts. We exchanged emails earlier. I know that I need to dump 
>>the schema from the
>>database before I do an upgrade on GUS.  I'm trying to use the script: 
>>dumpSchema.pl.
>>Essentially, the dba admin scripts need to be rebuilt to utilize the perl 
>>that's on this system.
>>
>>We're using code 3.0.  I can't find the old code anywhere.
>>
>>Regards,
>>
>>Marc
>>
>>
>>
>>
>>>From: "Michael Saffitz" <m...@sa...>
>>>To: "marc jackson" 
>>><de...@ho...>,<gus...@li...>
>>>Subject: Re: [GUSDEV] dba scripts
>>>Date: Mon, 16 Oct 2006 12:16:59 -0700
>>>
>>>
>>>Hi Marc,
>>>
>>>I think more information is needed here:
>>>
>>>1) Which dba scripts are you attempting to use?  What is occuring that 
>>>leads you to believe they are not working (i.e. can you paste the error 
>>>you're seeing?)
>>>
>>>2) What code base do you have at the moment? 3.0, 3.5?  I assume your DB 
>>>is 3.0, and you want to upgrade it to 3.5?  This is non-trivial, and you 
>>>should search the list archives for more information about general steps 
>>>and advice.
>>>
>>>--Mike
>>>
>>>----- Original Message ----- From: "marc jackson" <de...@ho...>
>>>To: <gus...@li...>
>>>Sent: Monday, October 16, 2006 6:37 AM
>>>Subject: [GUSDEV] dba scripts
>>>
>>>
>>>>Hello,
>>>>
>>>>I'm trying to do an upgrade from 3.0 to 3.5.
>>>>The dba scripts don't work [ possibly due to
>>>>a hard disk failure/faulty restore ]. Does
>>>>anyone know how to rebuid/recompile the
>>>>dba scripts.
>>>>
>>>>I ran build GUS -append, but this had no
>>>>effect.  I also re-installed Oracle 10.
>>>>
>>>>Regards,
>>>>
>>>>Marc
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------------------------
>>>>Using Tomcat but need to do more? Need to support web services, 
>>>>security?
>>>>Get stuff done quickly with pre-integrated technology to make your job 
>>>>easier
>>>>Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>>>>Geronimo
>>>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>
>>
>>
>>
>

Re: [GUSDEV] dba scripts

[Michael S. <m...@sa...>]

Hi Marc,

Ok,  I'd recommend getting 3.5.1 (or whatever the latest is), installing the 
app framework in a new location (just skip the step on installing the DB), 
and then using the dbaDumpSchema script.

3.0 is pretty old, and I'm not sure the extent that those admin scripts 
(i.e. dumpSchema) still work.

--Mike

----- Original Message ----- 
From: "marc jackson" <de...@ho...>
To: <m...@sa...>; <gus...@li...>
Sent: Monday, October 16, 2006 3:36 PM
Subject: Re: [GUSDEV] dba scripts


> Hi Michael,
>
> re: dba scripts. We exchanged emails earlier. I know that I need to dump 
> the schema from the
> database before I do an upgrade on GUS.  I'm trying to use the script: 
> dumpSchema.pl.
> Essentially, the dba admin scripts need to be rebuilt to utilize the perl 
> that's on this system.
>
> We're using code 3.0.  I can't find the old code anywhere.
>
> Regards,
>
> Marc
>
>
>
>
>>From: "Michael Saffitz" <m...@sa...>
>>To: "marc jackson" 
>><de...@ho...>,<gus...@li...>
>>Subject: Re: [GUSDEV] dba scripts
>>Date: Mon, 16 Oct 2006 12:16:59 -0700
>>
>>
>>Hi Marc,
>>
>>I think more information is needed here:
>>
>>1) Which dba scripts are you attempting to use?  What is occuring that 
>>leads you to believe they are not working (i.e. can you paste the error 
>>you're seeing?)
>>
>>2) What code base do you have at the moment? 3.0, 3.5?  I assume your DB 
>>is 3.0, and you want to upgrade it to 3.5?  This is non-trivial, and you 
>>should search the list archives for more information about general steps 
>>and advice.
>>
>>--Mike
>>
>>----- Original Message ----- From: "marc jackson" <de...@ho...>
>>To: <gus...@li...>
>>Sent: Monday, October 16, 2006 6:37 AM
>>Subject: [GUSDEV] dba scripts
>>
>>
>>>Hello,
>>>
>>>I'm trying to do an upgrade from 3.0 to 3.5.
>>>The dba scripts don't work [ possibly due to
>>>a hard disk failure/faulty restore ]. Does
>>>anyone know how to rebuid/recompile the
>>>dba scripts.
>>>
>>>I ran build GUS -append, but this had no
>>>effect.  I also re-installed Oracle 10.
>>>
>>>Regards,
>>>
>>>Marc
>>>
>>>
>>>
>>>-------------------------------------------------------------------------
>>>Using Tomcat but need to do more? Need to support web services, security?
>>>Get stuff done quickly with pre-integrated technology to make your job 
>>>easier
>>>Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>>>Geronimo
>>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>
>
> 

Re: [GUSDEV] dba scripts

[marc j. <de...@ho...>]

Hi Michael,

re: dba scripts. We exchanged emails earlier. I know that I need to dump the 
schema from the
database before I do an upgrade on GUS.  I'm trying to use the script: 
dumpSchema.pl.
Essentially, the dba admin scripts need to be rebuilt to utilize the perl 
that's on this system.

We're using code 3.0.  I can't find the old code anywhere.

Regards,

Marc




>From: "Michael Saffitz" <m...@sa...>
>To: "marc jackson" 
><de...@ho...>,<gus...@li...>
>Subject: Re: [GUSDEV] dba scripts
>Date: Mon, 16 Oct 2006 12:16:59 -0700
>
>
>Hi Marc,
>
>I think more information is needed here:
>
>1) Which dba scripts are you attempting to use?  What is occuring that 
>leads you to believe they are not working (i.e. can you paste the error 
>you're seeing?)
>
>2) What code base do you have at the moment? 3.0, 3.5?  I assume your DB is 
>3.0, and you want to upgrade it to 3.5?  This is non-trivial, and you 
>should search the list archives for more information about general steps 
>and advice.
>
>--Mike
>
>----- Original Message ----- From: "marc jackson" <de...@ho...>
>To: <gus...@li...>
>Sent: Monday, October 16, 2006 6:37 AM
>Subject: [GUSDEV] dba scripts
>
>
>>Hello,
>>
>>I'm trying to do an upgrade from 3.0 to 3.5.
>>The dba scripts don't work [ possibly due to
>>a hard disk failure/faulty restore ]. Does
>>anyone know how to rebuid/recompile the
>>dba scripts.
>>
>>I ran build GUS -append, but this had no
>>effect.  I also re-installed Oracle 10.
>>
>>Regards,
>>
>>Marc
>>
>>
>>
>>-------------------------------------------------------------------------
>>Using Tomcat but need to do more? Need to support web services, security?
>>Get stuff done quickly with pre-integrated technology to make your job 
>>easier
>>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[John I. <io...@pc...>]

Antonio,

I am building a GUS database using PostgreSQL, so I will likely  
encounter the same problem.  If so, I'll have to find a fix or  
workaround in the next few weeks.

Can you tell me more about what was happening when the error occurred?

Mike mentioned the install logs; do you still have those?  If so,  
please send me a copy.

There are some other people using GUS and PostgreSQL.  Do you know  
why they haven't encountered the error (or how they worked around it)?

Even if it isn't a problem for my project, I'll help if I can; part  
of my job is to contribute to the development of PostgreSQL GUS, so  
I'd like to see this fixed.  Email me (or the group) with any  
progress you make, and I'll do the same.

John Iodice

On Oct 16, 2006, at 3:12 PM, gusdev-gusdev- 
re...@li... wrote:
> Hello,
> did anyone have the time to look into the issue I submitted and  
> confirm it?
>
> Thank you very much,
>
> Antonio
>
> Quoting an...@ne...:
>
>> Quoting Michael Saffitz <m...@sa...>:
>>
>>> Antonio is correct here-- it looks like the postgres triggers  
>>> aren't being
>>> correctly generated for this table. I had thought I had fixed  
>>> this, but I
>>> guess not.  These are in the db writer for postgres within the db  
>>> admin
>>> package.  Search for 'ON INSERT TO'.  Antonio-- it may help if  
>>> you forward
>>> along your install logs (that include all SQL used in generating the
>>> instance).
>>> Steve's also correct-- bug 177 appears to track a different issue.
>>
>> I fear that while the database error does appear to be different, the
>> underlying issue is exactly the same.
>>
>> Following Steve's advice to try suggesting a fix, I've been  
>> digging further.
>> If I got your code correctly, all this wreck is generated when the  
>> schema
>> hierarchy gets converted, in
>>
>>  GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/ 
>> GusClassHierarchyConverter.java
>>
>> In function 'buildSuperClassView', (around line 440 in GUS 3.5; but
>> 'buildSubClassView' exhibits the same issue) the code goes like this:
>>
>> --------------------------------------------------------------------- 
>> -------
>> // Housekeeping Columns and complete for the Version View
>> if (impTable.isVersioned()) {
>>   superClassView.setVersioned(true);
>>   verSql = sql.concat(" ");
>>
>>   for (Iterator i = verHousekeepingColumns.iterator(); i.hasNext 
>> ();) {
>>     Column column = (Column)i.next();
>>     verSql = verSql.concat(", " + column.getName());
>>     superClassView.getVersionView().addColumn(new
>> ColumnPair(column.getName(),
>>              column.getName()));
>>   }
>>   verSql = verSql.concat(
>>     " FROM " +
>>     impTable.getVersionTable().getSchema().getName() +
>>     "." + impTable.getVersionTable().getName() +
>>     ";");
>>   superClassView.getVersionView().setSql(verSql);
>> }
>> --------------------------------------------------------------------- 
>> -------
>>
>> Now, the problem is that while 'verSql' is correctly generated  
>> (because it
>> starts with 'sql'), the original view's colums are not copied at all.
>>
>> The reason is that GusView behaves differently from GusTable,  
>> since its
>> 'setVersioned()' method does not copy the base view colums as one  
>> might have
>> expected after having looked at GusTable.
>>
>> As far as I can tell this has no relation to the actual database  
>> instance in
>> use, but I'd say that this is the core of the problem.
>>
>> HTH,
>>
>> Antonio
>>
>>
>> ----------------------------------------------------------------
>> Net Wise webmail system - http://www.netwise.it
>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to  
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>> opinions on IT & business topics through brief surveys -- and earn  
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>> page=join.php&p=sourceforge&CID=DEVDEV
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>> !DSPAM:452a0cfd138065873587180!
>>
>>
>
>
>
>
> ----------------------------------------------------------------
> Net Wise webmail system - http://www.netwise.it
> This message was sent using IMP, the Internet Messaging Program.

Re: [GUSDEV] dba scripts

[Michael S. <m...@sa...>]

Hi Marc,

I think more information is needed here:

1) Which dba scripts are you attempting to use?  What is occuring that leads 
you to believe they are not working (i.e. can you paste the error you're 
seeing?)

2) What code base do you have at the moment? 3.0, 3.5?  I assume your DB is 
3.0, and you want to upgrade it to 3.5?  This is non-trivial, and you should 
search the list archives for more information about general steps and 
advice.

--Mike

----- Original Message ----- 
From: "marc jackson" <de...@ho...>
To: <gus...@li...>
Sent: Monday, October 16, 2006 6:37 AM
Subject: [GUSDEV] dba scripts


> Hello,
>
> I'm trying to do an upgrade from 3.0 to 3.5.
> The dba scripts don't work [ possibly due to
> a hard disk failure/faulty restore ]. Does
> anyone know how to rebuid/recompile the
> dba scripts.
>
> I ran build GUS -append, but this had no
> effect.  I also re-installed Oracle 10.
>
> Regards,
>
> Marc
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job 
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

[GUSDEV] dba scripts

[marc j. <de...@ho...>]

Hello,

I'm trying to do an upgrade from 3.0 to 3.5.
The dba scripts don't work [ possibly due to
a hard disk failure/faulty restore ]. Does
anyone know how to rebuid/recompile the
dba scripts.

I ran build GUS -append, but this had no
effect.  I also re-installed Oracle 10.

Regards,

Marc