gusdev-gusdev — Topics concerning GUS development

[GUSDEV] LoadFastaSequences.pm

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

Folks:

I am trying to run the LoadFastaSequences.pm plugin to add a sequence.

The results from running LoadFastaSequences.pm --help are not very clear
to me.

According to the instructions only 3 attributes are required, but I found
that it is not so, Gus wants data for other attributes, I am up to 7 so
far and is asking for more.

Does anybody have a detailed listing with examples, of how Gus wants the
attributes when running the LoadFastaSequences.pm plugin?

Cheers,
Michael Robinson
Bioinformatics Research Group (BioRG)
Florida International University
Miami FL 33199

[GUSDEV] Using Plugin LoadFastaSequences

[<gi...@cs...>]

Hi folks:

Does anyone have some examples using GUS Plugins? My first goal (nothing
complicated, mind you!) is to load a simple sequence from a local file
into the database the command LoadFastaSequences. I have yet to figure ou=
t
how to successfully do this. Every variant I try, it seems to ask for new
information.

It seems to require a externalDatabaseName and Version even though I am
just trying to load a local file. So I made up a dummy name and version
number. Then it required me to figure out a regular expression for the
SourceId, which too was fine. Now it wants a regular expression for the
sequence_version.

Any pointers would be most appreciated.

--Giri Narasimhan, FIU

Re: [GUSDEV] PDB Format

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

Hi Adhemer,
We don't have a mechanism for storing (protein) structures in GUS. =20
For PlasmoDB as you noted we are just storing links.
My thoughts are that you might start with a separate schema to =20
capture structure as works best for you and then once you are happy =20
with it propose it as a new schema namespace for GUS.

Cheers,
Chris

Chris Stoeckert, Ph.D.
Research Associate 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 Jun 2, 2006, at 8:36 AM, Adhemar Zerlotini Neto wrote:

> Hello,
> I would like to know how to store new protein structures (.pdb =20
> format) in the GUS database.
> I saw that this information is being published in PlasmoDB, for =20
> example, but the protein structures are already submitted to the =20
> PDB. In our case, the structures weren't submitted yet and we would =20=

> like to show them through a viewer, like Cn3D.
> I=B4m looking forward to hearing from you.
> Thank you,
> Adhemar
>
>
> Adhemar Zerlotini Neto
> Schistosoma mansoni Database Project
> Centro de Pesquisas Ren=E9 Rachou - FIOCRUZ
> Av. Augusto de Lima 1715
> BH MG 30190-002, Brazil
> Phone: +55-31-3349-7798
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] PDB Format

[Adhemar Z. N. <ad...@cp...>]

Hello,<br />I would like to know how to store new protein structures (.pd=
b
format) in the GUS database.<br />I saw that this information is being
published in PlasmoDB, for example, but the protein structures are alread=
y
submitted to the PDB. In our case, the structures weren't submitted yet
and we would like to show them through a viewer, like Cn3D.<br />I=B4m
looking forward to hearing from you.<br />Thank you,<br />Adhemar <br
/><br /><br />Adhemar Zerlotini Neto<br /><span style=3D"font-style:
italic;">Schistosoma mansoni</span> Database Project<br />Centro de
Pesquisas Ren=E9 Rachou - FIOCRUZ<br />Av. Augusto de Lima 1715<br />BH M=
G
30190-002, Brazil<br />Phone: +55-31-3349-7798

Re: [GUSDEV] Plugin registration problem

[John E. B. <jbr...@pc...>]

I just had this same problem... the Revision #  for GusApplication 
was not automatically being updated by svn.

svn update GUS/PluginMgr/lib/perl/GusApplication.pm
build GUS/PluginMgr install -append
...
then retry your plugin

john


At 03:53 PM 6/1/2006, mro...@cs... wrote:
>Folks:
>
>We have successfully installed GUS. Now we are trying to run some sample
>Plugins. We know that before running any Plugins, they have to be
>"registered" using the +create option. But this registering process imply
>does not work.
>
>Regardless of whether I type in
> > ga +create GUS::Supported::Plugin::InsertControl --commit
>
>or
> > ga +create GUS::PluginMgr::Supported::LoadFastaSequences --commit
>
>we get the same error message, which is the following:
>
>"USER ERROR: GUS::PluginMgr::GusApplication has never been registered.
>  Please use 'ga +create GUS::PluginMgr::GusApplication --commit'
>"
>
>Note the the error message refers to the Plugin "GusApplication", which is
>not the one I am trying to register. So I followed the instructions and
>types in
> > ga +create GUS::PluginMgr::GusApplication --commit
>
>and I get the exact same error message. It is as if it ignores my command
>and giving me some standard error message, which I do not understand.
>Any light you can shed on this hurdle would be much appreciated.
>
>Cheers,
>Michael Robinson
>Bioinformatics Research Group (BioRG)
>Florida International University
>Miami FL 33199
>
>
>
>
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

thanks
john 

Re: [GUSDEV] Plugin registration problem

[Jian Lu <jl...@vb...>]

Do you run this command before registering plugins?

$ ga +meta --commit


mro...@cs... wrote:
> Folks:
>
> We have successfully installed GUS. Now we are trying to run some sample
> Plugins. We know that before running any Plugins, they have to be
> "registered" using the +create option. But this registering process imply
> does not work.
>
> Regardless of whether I type in
>   
>> ga +create GUS::Supported::Plugin::InsertControl --commit
>>     
>
> or
>   
>> ga +create GUS::PluginMgr::Supported::LoadFastaSequences --commit
>>     
>
> we get the same error message, which is the following:
>
> "USER ERROR: GUS::PluginMgr::GusApplication has never been registered.
>  Please use 'ga +create GUS::PluginMgr::GusApplication --commit'
> "
>
> Note the the error message refers to the Plugin "GusApplication", which is
> not the one I am trying to register. So I followed the instructions and
> types in
>   
>> ga +create GUS::PluginMgr::GusApplication --commit
>>     
>
> and I get the exact same error message. It is as if it ignores my command
> and giving me some standard error message, which I do not understand.
> Any light you can shed on this hurdle would be much appreciated.
>
> Cheers,
> Michael Robinson
> Bioinformatics Research Group (BioRG)
> Florida International University
> Miami FL 33199
>
>
>
>
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>   

[GUSDEV] Plugin registration problem

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

Folks:

We have successfully installed GUS. Now we are trying to run some sample
Plugins. We know that before running any Plugins, they have to be
"registered" using the +create option. But this registering process imply
does not work.

Regardless of whether I type in
> ga +create GUS::Supported::Plugin::InsertControl --commit

or
> ga +create GUS::PluginMgr::Supported::LoadFastaSequences --commit

we get the same error message, which is the following:

"USER ERROR: GUS::PluginMgr::GusApplication has never been registered.
 Please use 'ga +create GUS::PluginMgr::GusApplication --commit'
"

Note the the error message refers to the Plugin "GusApplication", which i=
s
not the one I am trying to register. So I followed the instructions and
types in
> ga +create GUS::PluginMgr::GusApplication --commit

and I get the exact same error message. It is as if it ignores my command
and giving me some standard error message, which I do not understand.
Any light you can shed on this hurdle would be much appreciated.

Cheers,
Michael Robinson
Bioinformatics Research Group (BioRG)
Florida International University
Miami FL 33199

Re: [GUSDEV] out of memory when loading taxonomy

[Jian Lu <jl...@vb...>]

Thanks for such detail guidance.

Here is the error message output:

Out of memory!
Issuing rollback() for database handle being DESTROY'd without explicit 
disconnect(), <MERGED> line 5401.
Issuing rollback() for database handle being DESTROY'd without explicit 
disconnect(), <MERGED> line 5401.

Database: Oracle 9i on Sun Solaris
Application: SuSE Linux Enterprise Server 9

By running ulimit -a, the output is 
core file size        (blocks, -c) 0
data seg size         (kbytes, -d) unlimited
file size             (blocks, -f) unlimited
max locked memory     (kbytes, -l) unlimited
max memory size       (kbytes, -m) unlimited
open files                    (-n) 1024
pipe size          (512 bytes, -p) 8
stack size            (kbytes, -s) unlimited
cpu time             (seconds, -t) unlimited
max user processes            (-u) 27636
virtual memory        (kbytes, -v) unlimited


My confusion is I used the same application to successfully load 
taxonomy to another database instance located on the same RDBMS machine. 
I didn't run them at the same time.

Fernan Aguero wrote:
> +----[ Jian Lu <jl...@vb...> (31.May.2006 10:45):
> |
> | Hi GUSDEV,
> | 
> | When I was using GUS plug-in to load NCBI taxonomy, it failed. The error 
> | message is 'Out of Memory'. My machine's RAM is 4G which should be 
> | enough to hold the data. Any hint would be appreciated. Thanks,
> | 
> | Jian
> |
> +----]
>
> Jian,
>
> can you post the exact error message (copy & paste)?
>
> Is it Perl running out of memory? Or is it the db
> (postgres/oracle)?
>
> Your box has 4Gb RAM, but this doesn't mean that all of this
> memory is available to the application.
>
> Are you running the plugin from one host and the db server
> in another host? If so, which one is 'getting out of
> memory'?
>
>
> What RDBMS are you using? Postgres? Oracle?
>
> Have you set up your RDBMS to use the extra available
> memory? Both Oracle and Postgres should be configured to use
> more memory, if it's available. The default configuration
> that (the one you get from a fresh install) would give you a
> horrid performance and will not make use of extra RAM.
>
>
> What OS are you using? Linux? FreeBSD? 
>
> Have you tuned the OS? (through building a new kernel or
> modifying kernel tunables using sysctl or something
> similar?) Raising maxusers, maxfiles and/or a number of
> kernel parameters can give your app more room to scale if
> necessary. 
>
>
> Is this a dedicated db server or is it running other
> applications alongside postgres or oracle? Even if you tune
> your db and OS to maximize the use of resources, running two
> or more apps that compete for the same resource will lead to
> degraded performance.
>
> As you can see, there are a number of steps that you should
> follow to make use of the available RAM and to optimize
> performance of your DB app. 
>
> And we need more information about your setup to be able to
> guess what the problem might be.
>
> Fernan
>
> PS: I've succesfully loaded NCBI Taxonomy (in ~ 2hs) on
> PostgreSQL running on a spare box that was not particularly
> beefy (AMD Sempron, 1 Gb RAM, RAID-1 ATA100). But both the OS
> (FreeBSD) and the application (PostgresSQL) were tuned to
> maximize use of available resources.
>   

Re: [GUSDEV] out of memory when loading taxonomy

[Jinal J. <jaj...@lb...>]

Hi Jian,

What are your ulimit settings? You can get it by typing "ulimit -a"



Thanks
--Jinal

On 5/31/06, Fernan Aguero <fe...@ii...> wrote:
>
> +----[ Jian Lu <jl...@vb...> (31.May.2006 10:45):
> |
> | Hi GUSDEV,
> |
> | When I was using GUS plug-in to load NCBI taxonomy, it failed. The error
> | message is 'Out of Memory'. My machine's RAM is 4G which should be
> | enough to hold the data. Any hint would be appreciated. Thanks,
> |
> | Jian
> |
> +----]
>
> Jian,
>
> can you post the exact error message (copy & paste)?
>
> Is it Perl running out of memory? Or is it the db
> (postgres/oracle)?
>
> Your box has 4Gb RAM, but this doesn't mean that all of this
> memory is available to the application.
>
> Are you running the plugin from one host and the db server
> in another host? If so, which one is 'getting out of
> memory'?
>
>
> What RDBMS are you using? Postgres? Oracle?
>
> Have you set up your RDBMS to use the extra available
> memory? Both Oracle and Postgres should be configured to use
> more memory, if it's available. The default configuration
> that (the one you get from a fresh install) would give you a
> horrid performance and will not make use of extra RAM.
>
>
> What OS are you using? Linux? FreeBSD?
>
> Have you tuned the OS? (through building a new kernel or
> modifying kernel tunables using sysctl or something
> similar?) Raising maxusers, maxfiles and/or a number of
> kernel parameters can give your app more room to scale if
> necessary.
>
>
> Is this a dedicated db server or is it running other
> applications alongside postgres or oracle? Even if you tune
> your db and OS to maximize the use of resources, running two
> or more apps that compete for the same resource will lead to
> degraded performance.
>
> As you can see, there are a number of steps that you should
> follow to make use of the available RAM and to optimize
> performance of your DB app.
>
> And we need more information about your setup to be able to
> guess what the problem might be.
>
> Fernan
>
> PS: I've succesfully loaded NCBI Taxonomy (in ~ 2hs) on
> PostgreSQL running on a spare box that was not particularly
> beefy (AMD Sempron, 1 Gb RAM, RAID-1 ATA100). But both the OS
> (FreeBSD) and the application (PostgresSQL) were tuned to
> maximize use of available resources.
>
>
> -------------------------------------------------------
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications in
> the hosting industry. Fanatical Support. Click to learn more
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] out of memory when loading taxonomy

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

+----[ Jian Lu <jl...@vb...> (31.May.2006 10:45):
|
| Hi GUSDEV,
| 
| When I was using GUS plug-in to load NCBI taxonomy, it failed. The error 
| message is 'Out of Memory'. My machine's RAM is 4G which should be 
| enough to hold the data. Any hint would be appreciated. Thanks,
| 
| Jian
|
+----]

Jian,

can you post the exact error message (copy & paste)?

Is it Perl running out of memory? Or is it the db
(postgres/oracle)?

Your box has 4Gb RAM, but this doesn't mean that all of this
memory is available to the application.

Are you running the plugin from one host and the db server
in another host? If so, which one is 'getting out of
memory'?


What RDBMS are you using? Postgres? Oracle?

Have you set up your RDBMS to use the extra available
memory? Both Oracle and Postgres should be configured to use
more memory, if it's available. The default configuration
that (the one you get from a fresh install) would give you a
horrid performance and will not make use of extra RAM.


What OS are you using? Linux? FreeBSD? 

Have you tuned the OS? (through building a new kernel or
modifying kernel tunables using sysctl or something
similar?) Raising maxusers, maxfiles and/or a number of
kernel parameters can give your app more room to scale if
necessary. 


Is this a dedicated db server or is it running other
applications alongside postgres or oracle? Even if you tune
your db and OS to maximize the use of resources, running two
or more apps that compete for the same resource will lead to
degraded performance.

As you can see, there are a number of steps that you should
follow to make use of the available RAM and to optimize
performance of your DB app. 

And we need more information about your setup to be able to
guess what the problem might be.

Fernan

PS: I've succesfully loaded NCBI Taxonomy (in ~ 2hs) on
PostgreSQL running on a spare box that was not particularly
beefy (AMD Sempron, 1 Gb RAM, RAID-1 ATA100). But both the OS
(FreeBSD) and the application (PostgresSQL) were tuned to
maximize use of available resources.

[GUSDEV] out of memory when loading taxonomy

[Jian Lu <jl...@vb...>]

Hi GUSDEV,

When I was using GUS plug-in to load NCBI taxonomy, it failed. The error 
message is 'Out of Memory'. My machine's RAM is 4G which should be 
enough to hold the data. Any hint would be appreciated. Thanks,

Jian

Re: [GUSDEV] Plugin's list and use samples

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

Michael,
if you go to

https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/

you should find in the plugin/ directory the currently supported plugins 
(most recent commits to svn). As far as I know, a supported plugin should 
work both with Oracle and with Postgres.
In the doc/ directory you'll find documentation for some of them. In any 
case, you should be able to generate html doc for any supported plugin by 
running it with the --helpHTML option.
The config/ directory contains a few sample configuration files for some 
of the plugins.
Elisabetta


---

On Tue, 30 May 2006 mro...@cs... wrote:

> Hello,
>
> This is my first email to the "gusdev group".
>
> I would like to find a list containing all GusDB supported Plugins,
> also detailed samples on how to use them.
>
> I am using the postgres database.
>
> I found some samples at https://www.vbi.vt.edu but they refer to oracle
> and were published in Jan 10, 2004.
>
> Thank you
>
> Michael Robinson
>
>
>
> -------------------------------------------------------
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications in
> the hosting industry. Fanatical Support. Click to learn more
> http://sel.as-us.falkag.net/sel?cmd_______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] Plugin's list and use samples

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

Hello,

This is my first email to the "gusdev group".

I would like to find a list containing all GusDB supported Plugins,
also detailed samples on how to use them.

I am using the postgres database.

I found some samples at https://www.vbi.vt.edu but they refer to oracle
and were published in Jan 10, 2004.

Thank you

Michael Robinson

Re: [GUSDEV] Question Regarding: InsertSequenceFeatures

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

+----[ Kumar, Sanjeev <San...@ng...> (16.May.2006 17:51):
|
| Hi Group,
|    I am having a problem in trapping the errors generated by
| InsertSequenceFeatures in a file.
|    When I am using " ga GUS::....> errorfile", it captures all other
| outputs except Error string / error   
|    description. So, it is not helpful.
|    Also, I tried to use parameter "--failDir", it didn't do any thing.
|    I am sure there must be a way, pl. guide me in finding.
|
+----]

Kumar, 

by doing 'ga ... > file' you're only redirecting stdout. 

If you want to redirect stderr you should do something like
'ga ... >& file.err'

If you want to redirect both, it will depend on the shell
you're using. For csh the following works for me:
( ga ... > file.stdout ) >& file.stderr

For bash, I'm sure Google will tell you :)

The other alternative is to use script(1) first and then run
all your commands within a script session.  When you exit
script (ctrl-d or just 'exit') everything (including all
output printed to stdout and stderr) will be in the file you
specified or in a file named 'typescript' in the current
directory.

Hope this helps,

fernan

[GUSDEV] (no subject)

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

try
ga GUS::.... 2> errorfile

(2 is the file descriptor for stderr)

> From: "Kumar, Sanjeev" <San...@ng...>
> Date: May 12, 2006 11:29:49 AM EDT
> To: <gus...@li...>
> Subject: [GUSDEV] Question Regarding: InsertSequenceFeatures
>
> Hi Group,
>    I am having a problem in trapping the errors generated by
> InsertSequenceFeatures in a file.
>    When I am using " ga GUS::....> errorfile", it captures all other
> outputs except Error string / error
>    description. So, it is not helpful.
>    Also, I tried to use parameter "--failDir", it didn't do any thing.
>    I am sure there must be a way, pl. guide me in finding.
>
> Thanks
> Sanjeev
>

[GUSDEV] Question Regarding: InsertSequenceFeatures

[Kumar, S. <San...@ng...>]

Hi Group,
   I am having a problem in trapping the errors generated by
InsertSequenceFeatures in a file.
   When I am using " ga GUS::....> errorfile", it captures all other
outputs except Error string / error  =20
   description. So, it is not helpful.
   Also, I tried to use parameter "--failDir", it didn't do any thing.
   I am sure there must be a way, pl. guide me in finding.

Thanks
Sanjeev =20

Re: [GUSDEV] bug #33 is marked as fixed but ...

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

+----[ Michael Saffitz <m...@sa...> (08.May.2006 19:31):
| 

[snipped]

| >But also, I thought that 'trunk' was the main line of
| >development, and thus that checking out code from 'trunk'
| >would get me the latest development snapshot as opposed to
| >getting code from a branch, which, well, being branched from the
| >'trunk' is supposed to carry a snapshot + fixes or
| >development made after branching. But this is all based on
| >my past experience with CVS.
| >
| >I'm not too familiar with svn but I was under the impression
| >that it was a drop-in replacement for CVS with additional
| >features.
| 
| Yes...  subversion is intended as a cvs replacement, and the assumption 
| that development occurs on the trunk is accurate... except in this case. 
|  This is due to historical reasons:  GUS had been a work in progress, 
| without discreet releases, and most people were thus used to working 
| directly in the trunk.  It was just easier to branch for development and 
| keep the trunk stable than change the community's behavior.

I see ... but maybe this could be changed in the future? It
gives a more smooth devel roadmap ... at least for me it's
easier to work with branches/tags, as it's always clear what
I'm getting when I choose to download/checkout from a
particular branch/tag.

Or, alternatively, do not branch the code. If people feel
more comfortable without discreet releases, then keep
development in the trunk and only 'tag' the tree at
particular times (a release), a major event (ie. a
publication), like it's been already done for GUS. In this
case branching creates a confusion (latest code in the
branch but not in the trunk), and a load on the maintainer
of the repository as s/he will have to merge back all the
changes to trunk when work in a new release starts ...

| >Which leads me to another question (to the SVN meisters):
| >how's the svn repository laid out, and how is the
| >development cycle mapped onto the repository? What's the
| >main line of development? Trunk?
| 
| At least when I was working on it (which was up to 1/06), trunk was 
| stable and branches/tags contained historical and dev releases.

OK.

| >When I browse https://www.cbil.upenn.edu/svn/gus/ I see 
| >'branches', 'tags' and 'trunk' which to me look pretty much
| >like CVS. That's why I supposed that 'trunk' was the main
| >line of development.
| >
| >Say you've already branched from trunk for 3.6, then any
| >change made into this branch would have to be merged back
| >into the trunk in order to be also incorporated into future
| >releases ... unless there's some svn magic I'm unaware of.
| 
| This is correct.

A nice load over the shoulders of the repository meister :)

| AFAIK/remember, Schema 3.6 is basically ready to go, but the 
| AppFramework components do not yet support it.  3.6 changes were marked 
| resolved, but not closed with the assumption that that would occur when 
| it was released.

Got it.

Thanks for the clarification. And good luck with your new
job! (I just knew about it)

Fernan

| 
| --Mike
|
+----]

Re: [GUSDEV] bug #33 is marked as fixed but ...

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

Comments below...

Fernan Aguero wrote:
> +----[ Mark Heiges <mh...@ug...> (08.May.2006 16:35):
> |
> | It's fixed in 3.6-Dev
> | 
> | $ svn log -r4310 https://cbil.upenn.edu/svn/gus/GusSchema/branches/ 
> | 3-6-Dev/
> | ------------------------------------------------------------------------
> | r4310 | msaffitz | 2005-12-11 12:20:06 -0500 (Sun, 11 Dec 2005) | 1 line
> | 
> | fix for 33, Schema changes to capture more information from dbEST and
> | ------------------------------------------------------------------------
> |
> +----]
> 
> Thanks Mark,
> 
> based on the followup comments for the bug I thought some of
> the changes ended up in 3.5.1.
> 
> But also, I thought that 'trunk' was the main line of
> development, and thus that checking out code from 'trunk'
> would get me the latest development snapshot as opposed to
> getting code from a branch, which, well, being branched from the
> 'trunk' is supposed to carry a snapshot + fixes or
> development made after branching. But this is all based on
> my past experience with CVS.
> 
> I'm not too familiar with svn but I was under the impression
> that it was a drop-in replacement for CVS with additional
> features.

Yes...  subversion is intended as a cvs replacement, and the assumption 
that development occurs on the trunk is accurate... except in this case. 
  This is due to historical reasons:  GUS had been a work in progress, 
without discreet releases, and most people were thus used to working 
directly in the trunk.  It was just easier to branch for development and 
keep the trunk stable than change the community's behavior.

> 
> Which leads me to another question (to the SVN meisters):
> how's the svn repository laid out, and how is the
> development cycle mapped onto the repository? What's the
> main line of development? Trunk?

At least when I was working on it (which was up to 1/06), trunk was 
stable and branches/tags contained historical and dev releases.

> 
> When I browse https://www.cbil.upenn.edu/svn/gus/ I see 
> 'branches', 'tags' and 'trunk' which to me look pretty much
> like CVS. That's why I supposed that 'trunk' was the main
> line of development.
> 
> Say you've already branched from trunk for 3.6, then any
> change made into this branch would have to be merged back
> into the trunk in order to be also incorporated into future
> releases ... unless there's some svn magic I'm unaware of.
> 

This is correct.

AFAIK/remember, Schema 3.6 is basically ready to go, but the 
AppFramework components do not yet support it.  3.6 changes were marked 
resolved, but not closed with the assumption that that would occur when 
it was released.

--Mike

> Fernan
> 

Re: [GUSDEV] bug #33 is marked as fixed but ...

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

+----[ Mark Heiges <mh...@ug...> (08.May.2006 16:35):
|
| It's fixed in 3.6-Dev
| 
| $ svn log -r4310 https://cbil.upenn.edu/svn/gus/GusSchema/branches/ 
| 3-6-Dev/
| ------------------------------------------------------------------------
| r4310 | msaffitz | 2005-12-11 12:20:06 -0500 (Sun, 11 Dec 2005) | 1 line
| 
| fix for 33, Schema changes to capture more information from dbEST and
| ------------------------------------------------------------------------
|
+----]

Thanks Mark,

based on the followup comments for the bug I thought some of
the changes ended up in 3.5.1.

But also, I thought that 'trunk' was the main line of
development, and thus that checking out code from 'trunk'
would get me the latest development snapshot as opposed to
getting code from a branch, which, well, being branched from the
'trunk' is supposed to carry a snapshot + fixes or
development made after branching. But this is all based on
my past experience with CVS.

I'm not too familiar with svn but I was under the impression
that it was a drop-in replacement for CVS with additional
features.

Which leads me to another question (to the SVN meisters):
how's the svn repository laid out, and how is the
development cycle mapped onto the repository? What's the
main line of development? Trunk?

When I browse https://www.cbil.upenn.edu/svn/gus/ I see 
'branches', 'tags' and 'trunk' which to me look pretty much
like CVS. That's why I supposed that 'trunk' was the main
line of development.

Say you've already branched from trunk for 3.6, then any
change made into this branch would have to be merged back
into the trunk in order to be also incorporated into future
releases ... unless there's some svn magic I'm unaware of.

Fernan

Re: [GUSDEV] bug #33 is marked as fixed but ...

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

It's fixed in 3.6-Dev

$ svn log -r4310 https://cbil.upenn.edu/svn/gus/GusSchema/branches/ 
3-6-Dev/
------------------------------------------------------------------------
r4310 | msaffitz | 2005-12-11 12:20:06 -0500 (Sun, 11 Dec 2005) | 1 line

fix for 33, Schema changes to capture more information from dbEST and
------------------------------------------------------------------------


On May 8, 2006, at 3:11 PM, Fernan Aguero wrote:

> Hi,
>
> I've just noticed that some of the columns that were
> proposed to be added in bug #33 are missing from my local
> GUS instance (svn checkout of Apr 11th, 2006, which I guess
> corresponds to 3.5.1).
>
> The bug was marked as 'fixed' in Dec 2005 ... how do I get
> a version of GUS with these changes?
>
> svn checkout https://www.cbil.upenn.edu/svn/gus/gusTrunk GUS
> didn't get those for me
>
> Fernan
>
>
>
>
> -------------------------------------------------------
> 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] bug #33 is marked as fixed but ...

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

Hi,

I've just noticed that some of the columns that were
proposed to be added in bug #33 are missing from my local
GUS instance (svn checkout of Apr 11th, 2006, which I guess
corresponds to 3.5.1).

The bug was marked as 'fixed' in Dec 2005 ... how do I get
a version of GUS with these changes? 

svn checkout https://www.cbil.upenn.edu/svn/gus/gusTrunk GUS
didn't get those for me

Fernan

Re: [GUSDEV] InsertSequenceFeature Issue in GUS3.5

[Ed R. <ero...@ug...>]

I had to go back and check on this.  Intron is not supported
by the Unflattener the way it is invoked by
InsertSequenceFeatures.  When we invoke the unflattener,
because the exons in CryptoDB's gbfile were implicit, we set
the unflattener attribute use_magic to true.  This creates
explicit representations of the exons implicitly present in
the encoding of our gene locations.

Unfortunately, use_magic also requires that we set the
structure type to "0" GENE->mRNA->exon
                                 ->CDS

To get the introns which are specifically encoded in your GB
file, you will need to set the structure type to 1 when the
unflattener is invoked.  I made a number of changes to the
plugin for some colleagues a while back so they could
dynamically choose whether or not to use magic and which kind
of structure they wanted to load.  These changes were never
checked into the official GUS release because they involved
significant changes to the commandline interface.  I will dig
up these changes and show you where to make the necessary
modifications.

-ed

---- Original message ----
>Date: Tue, 2 May 2006 11:23:55 -0400
>From: "Kumar, Sanjeev" <San...@ng...>  
>Subject: [GUSDEV] InsertSequenceFeature Issue in GUS3.5  
>To: <gus...@li...>
>
>   Hi Group,
>      I am having little problem with
>   InsertSequenceFeature in our environment.
>      It is loading all features from the genBank file
>   except "intron" feature. I tried to look into the
>   code and found that it is all together skipping the
>   "intron" feature from genBank file. Is that the
>   issue with "BioPerl"?
>
>   Did any one face this issue earlier?
>
>   The version of bioperl in our environment is :1.5.0
>   And I am using very first version of GUS3.5. Do we
>   have any subsequent release like GUS3.5.X?
>   And the file I am trying to load is related to
>   MICROSPORIDIA organism (NC_003238.gbf).
>   ------
>   The genBank2gus.xml has entry for the intron like
>   this:
>   <feature name="intron" table="DoTS::IntronFeature"
>   so="intron">
>       <qualifier name="allele" lost="true"/>
>       <qualifier name="citation"/>
>       <qualifier name="cons_splice"/>
>       <qualifier name="evidence"/>
>       <qualifier name="function"/>
>       <qualifier name="gene" specialcase="gene"/>
>       <qualifier name="label"/>
>       <qualifier name="locus_tag" column="source_id"/>
>       <qualifier name="map"/>
>       <qualifier name="note" specialcase="note"/>
>       <qualifier name="number" column="num"/>
>       <qualifier name="old_locus_tag" lost="true"/>
>       <qualifier name="standard_name"/>
>       <qualifier name="usedin"/>
>       <qualifier name="db_xref" specialcase="dbxref"/>
>     </feature>
>
>   And the intron entry in genBank file looks like
>   this:
>   gene            complement(52254..52444)
>                        /db_xref="GeneID:860376"
>                        /locus_tag="ECU09_0395"
>        CDS            
>   join(complement(52254..52409),complement(52442..52444))
>                        /db_xref="GI:19173160"
>                        /db_xref="GeneID:860376"
>                        /locus_tag="ECU09_0395"
>                        /codon_start=1
>                        /protein_id="NP_596963.1"
>                       
>   /translation="MGSRKTALVKTRLMRALKRNREIPAWKRMMKEHKGEYNRARRHW
>                        RSKKLKIY"
>                        /product="60S RIBOSOMAL PROTEIN
>   L39"
>        misc_feature   
>   join(complement(52260..52409),complement(52442..52444))
>                        /db_xref="CDD:11875"
>                        /locus_tag="ECU09_0395"
>                        /note="RPL39; Region: Ribosomal
>   protein L39E
>                        [Translation, ribosomal
>   structure and biogenesis]"
>        intron          complement(52410..52441)
>                        /locus_tag="ECU09_0395"
>                        /note="intron L39"
>
>   Any help will be appreciated.
>
>   Thanks
>   Sanjeev Kumar
>   Northrop Grumman
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

Re: [GUSDEV] Build issue

[John F F. I. <fl...@cs...>]

Steve Fischer wrote:
> have you checked the permissions on the core.algorithm table?

Yes, I did. The user gusdb has authorization for it, as expected.

This is why I wanted a more verbose build process, so I could see 
exactly where things are failing.

-John

-- 
John Flynn                              fl...@cs...
=========================================================
Systems and Network Administration             /\_/\
School of Computer Science                    ( O.O )
Florida International University               >   <

Re: [GUSDEV] Build issue

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

have you checked the permissions on the core.algorithm table?

steve

John F Flynn III wrote:

> Hmmm. Is there a way to make the build process more verbose so that I 
> can find out what exactly is failing?
>
> As far as I can tell, everything seems successful up to the point 
> where those compilation failures occur.
>
> -John
>
> Steve Fischer wrote:
>
>> john-
>>
>> as you might know gus provides a perl and a java object layer.   each 
>> gus table is represented by a perl object and by a java object.
>>
>> part of the intall process is a code-generation step that generates 3 
>> perl files and 3 java files per gus table.
>>
>> then, after that, the install compiles the generated java files.
>>
>> this compile error is during that compile.
>>
>> it means that the code generation step didn't work right.   in 
>> particular, what happened is that the code generator did not 
>> successfully get info from postgresql on what the type of the 
>> Core.Algorithm column is.
>>
>> i'm not certain, but, i think this is brought about when you have a 
>> correct list of all the gus tables and views is core.tableinfo (which 
>> is where the code-generator looks to find out what tables exist), 
>> but, that the actual tables are not accessible to the code 
>> generator.   this sometimes happens because of permissions.   so, you 
>> need to make sure that Core.Algorithm is defined and accessible.
>>
>> steve
>>
>> John F Flynn III wrote:
>>
>>> Hiya folks! This is John Flynn from the Florida International 
>>> University School of Computer Science. We are trying to build GUSdb 
>>> and are running into issues.
>>>
>>> Apologies if anyone sees this twice, but I opened a bugzilla bug and 
>>> no one has responded, so I'm assuming no one is listening over 
>>> there. Hopefully someone here can help us.
>>>
>>> I read the list through archives, so if anyone responds, please CC 
>>> me as well as the list so I see the message sooner. Thanks!
>>>
>>> Basically, the GUS build process fails with numerous compilation 
>>> errors.
>>>
>>>
>>> I ensured all the requirements were met, set up the database, and 
>>> set up the configuration file as follows:
>>>
>>> ==begin configuration file snippet==
>>> dbVendor=Postgres
>>> dbiDsn=dbi:Pg:dbname=gusdb;host=localhost
>>> jdbcDsn=jdbc:postgresql://localhost/gusdb
>>>
>>> # Login and Password to the RDBMS
>>>
>>> databaseLogin=gusdb
>>> databasePassword=<password here>
>>>
>>> # Username, group, and project info from the relevant Core tables
>>>
>>> userName=dba
>>> group=dba
>>> project=Database administration
>>>
>>> tablespace=GUS
>>> ==End configuration file snippet==
>>>
>>> Relevant software versions follow:
>>>
>>> CentOS 4.3
>>> J2SE 1.5
>>> Ant 1.6.5
>>> Postgresql 7.4
>>> Perl 5.8.5 with required modules
>>>
>>> Error output follows:
>>>
>>>
>>>      [echo] Installing GUS/Model
>>>     [javac] Compiling 1260 source files to
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/classes
>>>     [javac]
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:78: 
>>>
>>> cannot find symbol
>>>     [javac] symbol  : class notdefyet
>>>     [javac] location: class org.gusdb.model.Core.Algorithm_Row
>>>     [javac]     public void setModificationDate (notdefyet value)
>>>     [javac]                                      ^
>>>     [javac]
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:83: 
>>>
>>> cannot find symbol
>>>     [javac] symbol  : class notdefyet
>>>     [javac] location: class org.gusdb.model.Core.Algorithm_Row
>>>     [javac]     public notdefyet getModificationDate () { return
>>> (notdefyet)get_Attribute("modification_date"); }
>>>     [javac]            ^
>>>     [javac]
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:78: 
>>>
>>> cannot find symbol
>>>     [javac] symbol  : class notdefyet
>>>     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
>>>     [javac]     public void setModificationDate (notdefyet value)
>>>     [javac]                                      ^
>>>     [javac]
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:83: 
>>>
>>> cannot find symbol
>>>     [javac] symbol  : class notdefyet
>>>     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
>>>     [javac]     public notdefyet getModificationDate () { return
>>> (notdefyet)get_Attribute("modification_date"); }
>>>     [javac]            ^
>>>     [javac]
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:54: 
>>>
>>> cannot find symbol
>>>     [javac] symbol  : class notdefyet
>>>     [javac] location: class 
>>> org.gusdb.model.Core.AlgorithmInvocation_Row
>>>     [javac]     public void setStartTime (notdefyet value)
>>>     [javac]                               ^
>>>     [javac]
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:59: 
>>>
>>> cannot find symbol
>>>     [javac] symbol  : class notdefyet
>>>     [javac] location: class 
>>> org.gusdb.model.Core.AlgorithmInvocation_Row
>>>     [javac]     public notdefyet getStartTime () { return
>>> (notdefyet)get_Attribute("start_time"); }
>>>     [javac]            ^
>>> ....snipped; this goes on with similar errors for many pages...
>>>     [javac]            ^
>>>     [javac] Note: Some input files use unchecked or unsafe operations.
>>>     [javac] Note: Recompile with -Xlint:unchecked for details.
>>>     [javac] 100 errors
>>>
>>> BUILD FAILED
>>> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:28: 
>>> The following
>>> error occurred while executing this line:
>>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/build.xml:99: The 
>>> following
>>> error occurred while executing this line:
>>> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:259: The
>>> following error occurred while executing this line:
>>> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:278: 
>>> Compile
>>> failed; see the compiler error output for details.
>>>
>>> Total time: 18 seconds
>>>
>

Re: [GUSDEV] Build issue

[John F F. I. <fl...@cs...>]

Hmmm. Is there a way to make the build process more verbose so that I 
can find out what exactly is failing?

As far as I can tell, everything seems successful up to the point where 
those compilation failures occur.

-John

Steve Fischer wrote:
> john-
> 
> as you might know gus provides a perl and a java object layer.   each 
> gus table is represented by a perl object and by a java object.
> 
> part of the intall process is a code-generation step that generates 3 
> perl files and 3 java files per gus table.
> 
> then, after that, the install compiles the generated java files.
> 
> this compile error is during that compile.
> 
> it means that the code generation step didn't work right.   in 
> particular, what happened is that the code generator did not 
> successfully get info from postgresql on what the type of the 
> Core.Algorithm column is.
> 
> i'm not certain, but, i think this is brought about when you have a 
> correct list of all the gus tables and views is core.tableinfo (which is 
> where the code-generator looks to find out what tables exist), but, that 
> the actual tables are not accessible to the code generator.   this 
> sometimes happens because of permissions.   so, you need to make sure 
> that Core.Algorithm is defined and accessible.
> 
> steve
> 
> John F Flynn III wrote:
> 
>> Hiya folks! This is John Flynn from the Florida International 
>> University School of Computer Science. We are trying to build GUSdb 
>> and are running into issues.
>>
>> Apologies if anyone sees this twice, but I opened a bugzilla bug and 
>> no one has responded, so I'm assuming no one is listening over there. 
>> Hopefully someone here can help us.
>>
>> I read the list through archives, so if anyone responds, please CC me 
>> as well as the list so I see the message sooner. Thanks!
>>
>> Basically, the GUS build process fails with numerous compilation errors.
>>
>>
>> I ensured all the requirements were met, set up the database, and set 
>> up the configuration file as follows:
>>
>> ==begin configuration file snippet==
>> dbVendor=Postgres
>> dbiDsn=dbi:Pg:dbname=gusdb;host=localhost
>> jdbcDsn=jdbc:postgresql://localhost/gusdb
>>
>> # Login and Password to the RDBMS
>>
>> databaseLogin=gusdb
>> databasePassword=<password here>
>>
>> # Username, group, and project info from the relevant Core tables
>>
>> userName=dba
>> group=dba
>> project=Database administration
>>
>> tablespace=GUS
>> ==End configuration file snippet==
>>
>> Relevant software versions follow:
>>
>> CentOS 4.3
>> J2SE 1.5
>> Ant 1.6.5
>> Postgresql 7.4
>> Perl 5.8.5 with required modules
>>
>> Error output follows:
>>
>>
>>      [echo] Installing GUS/Model
>>     [javac] Compiling 1260 source files to
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/classes
>>     [javac]
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:78: 
>>
>> cannot find symbol
>>     [javac] symbol  : class notdefyet
>>     [javac] location: class org.gusdb.model.Core.Algorithm_Row
>>     [javac]     public void setModificationDate (notdefyet value)
>>     [javac]                                      ^
>>     [javac]
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:83: 
>>
>> cannot find symbol
>>     [javac] symbol  : class notdefyet
>>     [javac] location: class org.gusdb.model.Core.Algorithm_Row
>>     [javac]     public notdefyet getModificationDate () { return
>> (notdefyet)get_Attribute("modification_date"); }
>>     [javac]            ^
>>     [javac]
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:78: 
>>
>> cannot find symbol
>>     [javac] symbol  : class notdefyet
>>     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
>>     [javac]     public void setModificationDate (notdefyet value)
>>     [javac]                                      ^
>>     [javac]
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:83: 
>>
>> cannot find symbol
>>     [javac] symbol  : class notdefyet
>>     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
>>     [javac]     public notdefyet getModificationDate () { return
>> (notdefyet)get_Attribute("modification_date"); }
>>     [javac]            ^
>>     [javac]
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:54: 
>>
>> cannot find symbol
>>     [javac] symbol  : class notdefyet
>>     [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
>>     [javac]     public void setStartTime (notdefyet value)
>>     [javac]                               ^
>>     [javac]
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:59: 
>>
>> cannot find symbol
>>     [javac] symbol  : class notdefyet
>>     [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
>>     [javac]     public notdefyet getStartTime () { return
>> (notdefyet)get_Attribute("start_time"); }
>>     [javac]            ^
>> ....snipped; this goes on with similar errors for many pages...
>>     [javac]            ^
>>     [javac] Note: Some input files use unchecked or unsafe operations.
>>     [javac] Note: Recompile with -Xlint:unchecked for details.
>>     [javac] 100 errors
>>
>> BUILD FAILED
>> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:28: The 
>> following
>> error occurred while executing this line:
>> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/build.xml:99: The 
>> following
>> error occurred while executing this line:
>> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:259: The
>> following error occurred while executing this line:
>> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:278: 
>> Compile
>> failed; see the compiler error output for details.
>>
>> Total time: 18 seconds
>>

-- 
John Flynn                              fl...@cs...
=========================================================
Systems and Network Administration             /\_/\
School of Computer Science                    ( O.O )
Florida International University               >   <