gusdev-gusdev — Topics concerning GUS development

Re: [GUSDEV] Which plugin is for EMBL file loading?

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

right now it is NASequence specific.

but... i don't think it would take much to upgrade it to handle 
AASequence. 

volunteers?  (i can't do it any time soon)

also, the main thing about this plugin is that the mapping from input 
features to gus features is 100% configurable.

steve

Angel Pizarro wrote:

> A little more detail, We are trying to load IPI protein data, which is 
> in UniProt format, which looks like EMBL format. Will this plugin 
> instert AAsequence and features?
>
> Thanks,
> Angel
>
> Steve Fischer wrote:
>
>> GUS::Supported::Plugin::InsertSequenceFeatures
>>
>> use:
>>  % ga GUS::Supported::Plugin::InsertSequenceFeatures --help
>>
>> to find out more about it.
>>
>> steve
>>
>> Weichen Wu wrote:
>>
>>> Hi,
>>>
>>> Is there a plugin to load sequence files in EMBL format?
>>>
>>> Thanks,
>>> Weichen
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
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>>
>>
>>
>>
>>
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>
>
>
>

Re: [GUSDEV] Which plugin is for EMBL file loading?

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

A little more detail, We are trying to load IPI protein data, which is 
in UniProt format, which looks like EMBL format. Will this plugin 
instert AAsequence and features?

Thanks,
Angel

Steve Fischer wrote:

> GUS::Supported::Plugin::InsertSequenceFeatures
>
> use:
>  % ga GUS::Supported::Plugin::InsertSequenceFeatures --help
>
> to find out more about it.
>
> steve
>
> Weichen Wu wrote:
>
>> Hi,
>>
>> Is there a plugin to load sequence files in EMBL format?
>>
>> Thanks,
>> Weichen
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
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>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
> -------------------------------------------------------
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-- 

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

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

Re: [GUSDEV] Which plugin is for EMBL file loading?

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

Steve Fischer wrote:

> GUS::Supported::Plugin::InsertSequenceFeatures
>
> use:
>  % ga GUS::Supported::Plugin::InsertSequenceFeatures --help
>
> to find out more about it.
>
> steve
>
> Weichen Wu wrote:
>
>> Hi,
>>
>> Is there a plugin to load sequence files in EMBL format?
>>
>> Thanks,
>> Weichen
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Power Architecture Resource Center: Free content, downloads, 
>> discussions,
>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
> -------------------------------------------------------
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-- 

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

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

[GUSDEV] ** Repository Move Complete

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

The repository move is complete.  The new URL is:

https://svn.cbil.upenn.edu/{repos}

Where {repos} is one of gus, cbil, or apidb.

** IMPORTANT!  In your checked out copies (local workspaces) you will need
to run the following command at the root level of every checked out project:

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

The, run an svn info to make sure that the repository is set correctly.

Please let me know if you have any questions.

--Mike

P.S. I will now begin moving the remaining CVS repositories into SVN.  Also,
the SVN web interface is now out of date.  I expect to update this within a
few days. 

Re: [GUSDEV] Which plugin is for EMBL file loading?

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

GUS::Supported::Plugin::InsertSequenceFeatures

use:
  % ga GUS::Supported::Plugin::InsertSequenceFeatures --help

to find out more about it.

steve

Weichen Wu wrote:

> Hi,
>
> Is there a plugin to load sequence files in EMBL format?
>
> Thanks,
> Weichen
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] Which plugin is for EMBL file loading?

[Weichen W. <we...@se...>]

Hi,

Is there a plugin to load sequence files in EMBL format?

Thanks,
Weichen

[GUSDEV] bld command: less typing for 'build'

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

folks-

i have added a minor shortcut command called 'bld' to save a little typing.

Here is its usage:

[sfischer@hera bin]$ bld

Usage: bld project[/component]

  calls 'build project[/component] install -append'

[GUSDEV] migrate a gus3.0 oracle db to gus3.5 postgres?

[Michael C. <cha...@vc...>]

Does anyone have advice on how to migrate a gus3.0 oracle db to gus3.5 
postgres? My idea is:

We already have the 3.5 schema loaded in our postgres DB, all we need is 
the flat files (.csv, but seperated with tabs) exported from the Oracle 
DB and a copy of your Gus 3.0 schema. We should be able to create a new 
database, say gus30, load the old schema, load the files into it with 
something like:

copy <table> from '<path>' with NULL as '';

then, manually examine the differences in the two schemas and copy the 
tables from one database to the other that are the same, and (when they 
are different) make appropriate modifications before copying. However if 
the two schemata are radically different this may not be feasible. Does 
anyone know how different they are?

Re: [GUSDEV] GUS 3.5

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

Hello,

GUS 3.5 can be used with either Oracle 9i/10g or with Postgres.  Oracle is
more established in so far as it has historically been the platform that GUS
has been developed against.

--Mike



On 10/3/05 12:48 PM, "Dhivya Arasappan/O/VCU" <ara...@vc...> wrote:

> Hi,
>  
> I have a question about GUS 3.5. I know that it provides compatability for
> PostGreSql but can it also be used with Oracle 9i? Or can we use it only with
> PostGres??
>  
> Any input on this would be appreciated,
> thanks
> dhivya 
> ------------------------------------------------------- This SF.Net email is
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] GUS 3.5

[Dhivya Arasappan/O/V. <ara...@vc...>]

<FONT face=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=
=3D2><div>Hi,</div><DIV>&nbsp;</DIV><DIV>I have a question about GUS 3.5. I=
 know that it provides compatability for PostGreSql but can it also be used=
 with Oracle 9i? Or can we use it only with PostGres??</DIV><DIV>&nbsp;</DI=
V><DIV>Any input on this would be appreciated,</DIV><DIV>thanks</DIV><DIV>d=
hivya </DIV></FONT>=

[GUSDEV] SVN/CVS Repository Changes

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

Two repository changes to note, both occurring Tuesday morning.

* The Subversion (SVN) repositories will be moving to a new server.  This
will result in about 15 minutes of downtime.  I will be making this move at
10:00am EST Tuesday.

The new URL will be:

https://svn.cbil.upenn.edu/{repos}/

Instead of the current:

https://www.cbil.upenn.edu/svn/{repos}/

* All older CVS repositories will be moving to subversion.  I will begin
this immediately following the subversion move detailed above.  PLEASE MAKE
SURE ALL CVS REVISISIONS ARE COMMITTED BY 9AM TUE MORNING!

Please let me know if you have any questions.

--Mike

[GUSDEV] Database Drivers in GUS

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

Note:

Here at CBIL, we've recently switched to use the Oracle OCI drivers for
database connections (instead of the pure-Java thin drivers).  While the OCI
drivers provide some additional necessary functionality for us, we've run in
to an issue that the underlying C libraries for OCI can only be loaded once
in each class loader.

This has created an issue particularly when running under Tomcat-- Tomcat
recommends there be one single OCI jar for the entire server; our model is
to have each webapp have lib coming as a symlink from the GUS home.  Of
course, the OCI jars could be removed from the GUS homes, but this would
cause compile issues as well as affect non-tomcat functionality (i.e. WDK
cli access).

The solution we've devised is to create a db_driver directory in each
lib/java directory that will contain Postgres and Oracle drivers.  This way,
the non Tomcat utilities can directly access the requisite jars, and they
will not be visable to Tomcat.

All project components that use DB drivers should conform to this new
policy, since they have the potential to impact other projects that need
this structure.

If there are suggestions for a better way to address this, we'd really
appreciate the feedback.

Thanks,

Mike

Re: [GUSDEV] WDK and GUS

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

The GUS system is a database and an application framework to load data 
into the database.

The WDK is a system that helps create a web front-end on top of GUS.

steve

xme...@ao... wrote:

>  
>  
>   I am really new to GUS and I have a couple of questions.  I noticed 
> there is a download for
>   GUS and for the WDK.  What is the difference?
>  
>   How do I know which one I need if I wanted to implement a 
> Bioinformatic data-mining website based
>   upon the GUS schema?
>  
>  
>   -KQ

[GUSDEV] WDK and GUS

[<xme...@ao...>]

 
 
  I am really new to GUS and I have a couple of questions.  I noticed there is a download for 
  GUS and for the WDK.  What is the difference?
 
  How do I know which one I need if I wanted to implement a Bioinformatic data-mining website based
  upon the GUS schema?
 
 
  -KQ

Re: [GUSDEV] ISF testing

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

henrique-

oops, sorry about that.  it was under a bit of construction today.   you=20
caught it when it was temporarily broken.  get the latest, which fixes=20
that problem.  (it will have occasional problems like this as it=20
continues to stabilize of the next week or so)

as always, be sure to get all of GUS/Supported, not just that one file.

steve

Henrique Juc=E1 wrote:

>Hi,
>
>Trying to test ISF plugin. This is the output I received....
>
>[juca@desterrensis Plugin]$ ga
>GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
>/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile
>/home/juca/GUS-Files/ISF/Z_mobilis.fasta --fileFormat genbank
>--extDbName 'TESTE' --extDbRlsVer '2005-09-06' --soCvsVersion 1.42
>Fri Sep 23 17:10:01 2005        ARGS    algoinvo        1
>Fri Sep 23 17:10:01 2005        ARGS    comment
>Fri Sep 23 17:10:01 2005        ARGS    commit  0
>Fri Sep 23 17:10:01 2005        ARGS    debug   0
>Fri Sep 23 17:10:01 2005        ARGS    defaultOrganism
>Fri Sep 23 17:10:01 2005        ARGS    description
>Fri Sep 23 17:10:01 2005        ARGS    downloadURL
>Fri Sep 23 17:10:01 2005        ARGS    extDbName       TESTE
>Fri Sep 23 17:10:01 2005        ARGS    extDbRlsDate
>Fri Sep 23 17:10:01 2005        ARGS    extDbRlsVer     2005-09-06
>Fri Sep 23 17:10:01 2005        ARGS    failDir
>Fri Sep 23 17:10:01 2005        ARGS    fileFormat      genbank
>Fri Sep 23 17:10:01 2005        ARGS    filename
>Fri Sep 23 17:10:01 2005        ARGS    gff2GroupTag    GenePrediction  =
Gene
>Fri Sep 23 17:10:01 2005        ARGS    gffFormat       2
>Fri Sep 23 17:10:01 2005        ARGS    group
>Fri Sep 23 17:10:01 2005        ARGS    gusconfigfile =20
>/usr/local/GUS/gus.properties
>Fri Sep 23 17:10:01 2005        ARGS    help
>Fri Sep 23 17:10:01 2005        ARGS    helpHTML
>Fri Sep 23 17:10:01 2005        ARGS    isUpdateMode    0
>Fri Sep 23 17:10:01 2005        ARGS    mapFile
>/home/juca/GUS-Files/ISF/genbank2gus.xml
>Fri Sep 23 17:10:01 2005        ARGS    naSequenceSubclass
>Fri Sep 23 17:10:01 2005        ARGS    project
>Fri Sep 23 17:10:01 2005        ARGS    projectName
>Fri Sep 23 17:10:01 2005        ARGS    restartPoint
>Fri Sep 23 17:10:01 2005        ARGS    seqFile
>/home/juca/GUS-Files/ISF/Z_mobilis.fasta
>Fri Sep 23 17:10:01 2005        ARGS    seqIdColumn     source_id
>Fri Sep 23 17:10:01 2005        ARGS    seqSoTerm
>Fri Sep 23 17:10:01 2005        ARGS    seqType
>Fri Sep 23 17:10:01 2005        ARGS    soCvsVersion    1.42
>Fri Sep 23 17:10:01 2005        ARGS    sqlVerbose      0
>Fri Sep 23 17:10:01 2005        ARGS    testNumber
>Fri Sep 23 17:10:01 2005        ARGS    user
>Fri Sep 23 17:10:01 2005        ARGS    verbose 0
>Fri Sep 23 17:10:01 2005        ARGS    veryVerbose     0
>Fri Sep 23 17:10:01 2005        COMMIT  commit off
>Fri Sep 23 17:10:01 2005        ALGINVID        104
>
>ERROR:
>Cannot import or construct new object for qualifier handler class
>'GUS::Supported::SpecialCaseQualifierHandlers'
>Can't modify constant item in scalar assignment at (eval 24) line 1, nea=
r "))"
>Bareword "GUS::Supported::Plugin::InsertSequenceFeatures" not allowed
>while "strict subs" in use at (eval 24)  line 1.
>
>STACK TRACE:
> at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.=
pm
>line 73        GUS::Supported::BioperlFeatMapperSet::_parseMapFile('GUS:=
:Supported::BioperlFeatMapperSet=3DHASH(0x9486
>68c)', '/home/juca/GUS-Files/ISF/genbank2gus.xml',
>'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a2 4160)')
>called at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapp=
erSet.pm
>line 17        GUS::Supported::BioperlFeatMapperSet::new('GUS::Supported=
::BioperlFeatMapperSet',
>'/home/juca/GUS-Fil es/ISF/genbank2gus.xml',
>'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a24160)')
>called at /usr/loc
>al/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>line 335      =20
>GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu=
gin::InsertSequenceFeatures=3DH
>ASH(0x8a24160)', 'HASH(0x9486608)') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.p m line
>469
>eval {...} called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
>461        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS:=
:PluginMgr::GusApplication=3DHASH(0x84d7c2
>0)', 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>/usr/local/GUS/gus_home/lib/perl/GUS/Plug inMgr/GusApplication.pm line
>380        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginM=
gr::GusApplication=3DHASH(0x84d7c20)',
>'GU S::Supported::Plugin::InsertSequenceFeatures') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusAp plication.pm line
>288        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::=
GusApplication=3DHASH(0x84d7c20)',
>'GUS::S upported::Plugin::InsertSequenceFeatures') called at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplic ation.pm line
>197        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::=
GusApplication=3DHASH(0x84d7c20)',
>'ARRAY( 0x84eb568)') called at /usr/local/GUS/gus_home/bin/ga line 11
>
>
>Hope it helps debugging...
>
>
>
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by:
>Tame your development challenges with Apache's Geronimo App Server.=20
>Download it for free - -and be entered to win a 42" plasma tv or your ve=
ry
>own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.ph=
p
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

Re: [GUSDEV] ISF release

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

Why are you using the "mutant" install?  If your schema is 3.5, you should
be using either the trunk, or the download from the GUS website.  If your
not using 3.5 (which I recommend, of course), then you probably shouldn't
use ISF since (Steve correct me if this is wrong) it's been designed for
3.5+ only.

There haven't been any major difficulties installing 3.5.  If do you use th=
e
trunk, you'll also need to get GusSchema.

This is correct:

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

--Mike

On 9/23/05 4:30 PM, "Henrique Juc=E1" <hen...@gm...> wrote:

> Thanks for the quick answers.
>=20
> Well, I did update all files needed by ISF plugin, as Steve instructed
> me a while ago. However, I'm not updating all GUS as a whole, since
> the version installed here is somewhat "mutant" - it comes from a
> mixture of the old tar.gz from the homepage and from manual updating
> of several files...
> Is the installation from
> "svn checkout https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk
> GUS" working?
>=20
> I do remember people here having some trouble trying to install from it.
>=20
>=20
>=20
>=20
> Kindest regards,
>=20
>=20
>=20
> Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>=20
> "As soon as you concern yourself with the "good" and "bad" of your fellow=
s,
> you create an opening in your heart for maliciousness to enter. Testing,
> competing with, and criticizing others weaken and defeat you."
>=20
> Morihei Ueshiba, O-Sensei (1883-1969)
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.
> Download it for free - -and be entered to win a 42" plasma tv or your ver=
y
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> _______________________________________________
> Gusdev-gusdev mailing list
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] ISF release

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

Thanks for the quick answers.

Well, I did update all files needed by ISF plugin, as Steve instructed
me a while ago. However, I'm not updating all GUS as a whole, since
the version installed here is somewhat "mutant" - it comes from a
mixture of the old tar.gz from the homepage and from manual updating
of several files...
Is the installation from
"svn checkout https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk
GUS" working?

I do remember people here having some trouble trying to install from it.




Kindest regards,



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

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

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] ISF release

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

Before anything else, make sure you do an svn update so that you're working
from the latest version.

--Mike


On 9/23/05 4:15 PM, "Steve Fischer" <sfi...@pc...> wrote:

> henrique-
>=20
> thanks for reporting this.   we have seen this before.   it is a mystery
> why subversion fails sometimes to fill that in.
>=20
> we'll look into it.
>=20
> steve
>=20
> Henrique Juc=E1 wrote:
>=20
>> Hi everyone...
>>=20
>>=20
>> I just downloaded every file needed for ISF, rebuilded GUS, and when I
>> tried to upload some files in my database, it printed the following
>> message:
>>=20
>> ga GUS::Supported::Plugin::InsertSequenceFeatures - -mapfile
>> /home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile /home/juca/GUS-File
>> s/ISF/Z_mobilis.fasta --fileFormat genbank --extDbName 'TESTE'
>> --extDbRlsVer '2 005-09-06' --soCvsVersion 1.42
>> The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
>> include a revision number, then the plugin has never been checked into
>> CVS.  Please do so to give it an intial revision at
>> /usr/local/GUS/gus_home/lib/perl/GUS/Plugin Mgr/Plugin.pm line 347.
>> Issuing rollback() for database handle being DESTROY'd without
>> explicit disconn ect().
>>=20
>> I had to enter ISF .pm archive and fill that line myself, but CVS
>> should do it, shouldn't it?
>>=20
>>=20
>> Thanks and nice weekend,
>>=20
>>=20
>> --
>> Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>>=20
>> "As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>> you create an opening in your heart for maliciousness to enter. Testing,
>> competing with, and criticizing others weaken and defeat you."
>>=20
>> Morihei Ueshiba, O-Sensei (1883-1969)
>>=20
>>=20
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App Server.
>> Download it for free - -and be entered to win a 42" plasma tv or your ve=
ry
>> own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.ph=
p
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> =20
>>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.
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Re: [GUSDEV] ISF release

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

henrique-

thanks for reporting this.   we have seen this before.   it is a mystery=20
why subversion fails sometimes to fill that in.

we'll look into it.

steve

Henrique Juc=E1 wrote:

>Hi everyone...
>
>
>I just downloaded every file needed for ISF, rebuilded GUS, and when I
>tried to upload some files in my database, it printed the following
>message:
>
>ga GUS::Supported::Plugin::InsertSequenceFeatures - -mapfile
>/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile /home/juca/GUS-File
>s/ISF/Z_mobilis.fasta --fileFormat genbank --extDbName 'TESTE'
>--extDbRlsVer '2 005-09-06' --soCvsVersion 1.42
>The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
>include a revision number, then the plugin has never been checked into
>CVS.  Please do so to give it an intial revision at
>/usr/local/GUS/gus_home/lib/perl/GUS/Plugin Mgr/Plugin.pm line 347.
>Issuing rollback() for database handle being DESTROY'd without
>explicit disconn ect().
>
>I had to enter ISF .pm archive and fill that line myself, but CVS
>should do it, shouldn't it?
>
>
>Thanks and nice weekend,
>
>
>--
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by:
>Tame your development challenges with Apache's Geronimo App Server.=20
>Download it for free - -and be entered to win a 42" plasma tv or your ve=
ry
>own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.ph=
p
>_______________________________________________
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>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

[GUSDEV] ISF testing

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

Hi,

Trying to test ISF plugin. This is the output I received....

[juca@desterrensis Plugin]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile
/home/juca/GUS-Files/ISF/Z_mobilis.fasta --fileFormat genbank
--extDbName 'TESTE' --extDbRlsVer '2005-09-06' --soCvsVersion 1.42
Fri Sep 23 17:10:01 2005        ARGS    algoinvo        1
Fri Sep 23 17:10:01 2005        ARGS    comment
Fri Sep 23 17:10:01 2005        ARGS    commit  0
Fri Sep 23 17:10:01 2005        ARGS    debug   0
Fri Sep 23 17:10:01 2005        ARGS    defaultOrganism
Fri Sep 23 17:10:01 2005        ARGS    description
Fri Sep 23 17:10:01 2005        ARGS    downloadURL
Fri Sep 23 17:10:01 2005        ARGS    extDbName       TESTE
Fri Sep 23 17:10:01 2005        ARGS    extDbRlsDate
Fri Sep 23 17:10:01 2005        ARGS    extDbRlsVer     2005-09-06
Fri Sep 23 17:10:01 2005        ARGS    failDir
Fri Sep 23 17:10:01 2005        ARGS    fileFormat      genbank
Fri Sep 23 17:10:01 2005        ARGS    filename
Fri Sep 23 17:10:01 2005        ARGS    gff2GroupTag    GenePrediction  Gen=
e
Fri Sep 23 17:10:01 2005        ARGS    gffFormat       2
Fri Sep 23 17:10:01 2005        ARGS    group
Fri Sep 23 17:10:01 2005        ARGS    gusconfigfile =20
/usr/local/GUS/gus.properties
Fri Sep 23 17:10:01 2005        ARGS    help
Fri Sep 23 17:10:01 2005        ARGS    helpHTML
Fri Sep 23 17:10:01 2005        ARGS    isUpdateMode    0
Fri Sep 23 17:10:01 2005        ARGS    mapFile
/home/juca/GUS-Files/ISF/genbank2gus.xml
Fri Sep 23 17:10:01 2005        ARGS    naSequenceSubclass
Fri Sep 23 17:10:01 2005        ARGS    project
Fri Sep 23 17:10:01 2005        ARGS    projectName
Fri Sep 23 17:10:01 2005        ARGS    restartPoint
Fri Sep 23 17:10:01 2005        ARGS    seqFile
/home/juca/GUS-Files/ISF/Z_mobilis.fasta
Fri Sep 23 17:10:01 2005        ARGS    seqIdColumn     source_id
Fri Sep 23 17:10:01 2005        ARGS    seqSoTerm
Fri Sep 23 17:10:01 2005        ARGS    seqType
Fri Sep 23 17:10:01 2005        ARGS    soCvsVersion    1.42
Fri Sep 23 17:10:01 2005        ARGS    sqlVerbose      0
Fri Sep 23 17:10:01 2005        ARGS    testNumber
Fri Sep 23 17:10:01 2005        ARGS    user
Fri Sep 23 17:10:01 2005        ARGS    verbose 0
Fri Sep 23 17:10:01 2005        ARGS    veryVerbose     0
Fri Sep 23 17:10:01 2005        COMMIT  commit off
Fri Sep 23 17:10:01 2005        ALGINVID        104

ERROR:
Cannot import or construct new object for qualifier handler class
'GUS::Supported::SpecialCaseQualifierHandlers'
Can't modify constant item in scalar assignment at (eval 24) line 1, near "=
))"
Bareword "GUS::Supported::Plugin::InsertSequenceFeatures" not allowed
while "strict subs" in use at (eval 24)  line 1.

STACK TRACE:
 at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
line 73        GUS::Supported::BioperlFeatMapperSet::_parseMapFile('GUS::Su=
pported::BioperlFeatMapperSet=3DHASH(0x9486
68c)', '/home/juca/GUS-Files/ISF/genbank2gus.xml',
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a2 4160)')
called at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperS=
et.pm
line 17        GUS::Supported::BioperlFeatMapperSet::new('GUS::Supported::B=
ioperlFeatMapperSet',
'/home/juca/GUS-Fil es/ISF/genbank2gus.xml',
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a24160)')
called at /usr/loc
al/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 335      =20
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DH
ASH(0x8a24160)', 'HASH(0x9486608)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.p m line
469
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
461        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Pl=
uginMgr::GusApplication=3DHASH(0x84d7c2
0)', 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/usr/local/GUS/gus_home/lib/perl/GUS/Plug inMgr/GusApplication.pm line
380        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr:=
:GusApplication=3DHASH(0x84d7c20)',
'GU S::Supported::Plugin::InsertSequenceFeatures') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusAp plication.pm line
288        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::Gus=
Application=3DHASH(0x84d7c20)',
'GUS::S upported::Plugin::InsertSequenceFeatures') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplic ation.pm line
197        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::Gus=
Application=3DHASH(0x84d7c20)',
'ARRAY( 0x84eb568)') called at /usr/local/GUS/gus_home/bin/ga line 11


Hope it helps debugging...



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

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

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] ISF release

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

Hi everyone...


I just downloaded every file needed for ISF, rebuilded GUS, and when I
tried to upload some files in my database, it printed the following
message:

ga GUS::Supported::Plugin::InsertSequenceFeatures - -mapfile
/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile /home/juca/GUS-File
s/ISF/Z_mobilis.fasta --fileFormat genbank --extDbName 'TESTE'
--extDbRlsVer '2 005-09-06' --soCvsVersion 1.42
The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
include a revision number, then the plugin has never been checked into
CVS.  Please do so to give it an intial revision at
/usr/local/GUS/gus_home/lib/perl/GUS/Plugin Mgr/Plugin.pm line 347.
Issuing rollback() for database handle being DESTROY'd without
explicit disconn ect().

I had to enter ISF .pm archive and fill that line myself, but CVS
should do it, shouldn't it?


Thanks and nice weekend,


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

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

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] questions on GUS::Supported::Plugin::InsertSequenceFeatures

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

Jian-

great...

can you send snippets of your input file that show examples of the data 
that is not being handled?

thanks,
steve

Jian Lu wrote:

> I have successfully run InsertSequenceFeatures for Genbank file.
>
> However, I have a few questions:
> 1) how does this plugin deal with sequence GI number? It seems it 
> didn't load GI number to SECONDARY_IDENTIFIER on 
> DoTS.ExternalNASequence. For example, for AE011191, GI:20520280 is 
> missed.
> 2) how does this plugin deal with locus_tag? It doesn't load locus_tag 
> to SOURCE_ID on all NA feature tables such as DoTS.Transcript.
> 3) how does this plugin deal with sequence topology?
>
>
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures 
> --mapFile=$GUS_HOME/config/genbank2gus.x
> ml --seqFile=/home/data/BRC_genomes/bacillus/AE011191 
> --fileFormat=genbank --extDbName=GenBank --extDbRlsVer=138
> --soCvsVersion 1.48 --seqType=DNA --commit
> Maximum number of  objects set to 500000
> Maximum number of  objects set to 500000
> Thu Sep 22 15:10:54 2005        ARGS    algoinvo        1
> Thu Sep 22 15:10:54 2005        ARGS    comment
> Thu Sep 22 15:10:54 2005        ARGS    commit  1
> Thu Sep 22 15:10:54 2005        ARGS    debug   0
> Thu Sep 22 15:10:54 2005        ARGS    defaultOrganism
> Thu Sep 22 15:10:54 2005        ARGS    description
> Thu Sep 22 15:10:54 2005        ARGS    downloadURL
> Thu Sep 22 15:10:54 2005        ARGS    extDbName       GenBank
> Thu Sep 22 15:10:54 2005        ARGS    extDbRlsDate
> Thu Sep 22 15:10:54 2005        ARGS    extDbRlsVer     138
> Thu Sep 22 15:10:54 2005        ARGS    failDir
> Thu Sep 22 15:10:54 2005        ARGS    fileFormat      genbank
> Thu Sep 22 15:10:54 2005        ARGS    filename
> Thu Sep 22 15:10:54 2005        ARGS    gff2GroupTag    
> GenePrediction  Gene
> Thu Sep 22 15:10:54 2005        ARGS    gffFormat       2
> Thu Sep 22 15:10:54 2005        ARGS    group
> Thu Sep 22 15:10:54 2005        ARGS    gusconfigfile   
> /home/brcgusts/GUS/gus_home/.gus.properties
> Thu Sep 22 15:10:54 2005        ARGS    help
> Thu Sep 22 15:10:54 2005        ARGS    helpHTML
> Thu Sep 22 15:10:54 2005        ARGS    isUpdateMode    0
> Thu Sep 22 15:10:54 2005        ARGS    mapFile 
> /home/brcgusts/GUS/gus_home/config/genbank2gus.xml
> Thu Sep 22 15:10:54 2005        ARGS    naSequenceSubclass
> Thu Sep 22 15:10:54 2005        ARGS    project
> Thu Sep 22 15:10:54 2005        ARGS    projectName
> Thu Sep 22 15:10:54 2005        ARGS    restartPoint
> Thu Sep 22 15:10:54 2005        ARGS    seqFile 
> /home/data/BRC_genomes/bacillus/AE011191
> Thu Sep 22 15:10:54 2005        ARGS    seqIdColumn     source_id
> Thu Sep 22 15:10:54 2005        ARGS    seqSoTerm
> Thu Sep 22 15:10:54 2005        ARGS    seqType DNA
> Thu Sep 22 15:10:54 2005        ARGS    soCvsVersion    1.48
> Thu Sep 22 15:10:54 2005        ARGS    sqlVerbose      0
> Thu Sep 22 15:10:54 2005        ARGS    testNumber
> Thu Sep 22 15:10:54 2005        ARGS    user
> Thu Sep 22 15:10:54 2005        ARGS    verbose 0
> Thu Sep 22 15:10:54 2005        ARGS    veryVerbose     0
> Thu Sep 22 15:10:54 2005        COMMIT  commit on
> Thu Sep 22 15:10:54 2005        ALGINVID        4362
> Thu Sep 22 15:11:09 2005        Inserted 100 feature trees
> Thu Sep 22 15:11:11 2005        RESULT  Processed: 
> /home/data/BRC_genomes/bacillus/AE011191 : genbank
>         Seqs Inserted: 1
>         Features Inserted: 426
>         Feature Trees Inserted: 114
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. 
> Download it for free - -and be entered to win a 42" plasma tv or your 
> very
> own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] questions on GUS::Supported::Plugin::InsertSequenceFeatures

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

I have successfully run InsertSequenceFeatures for Genbank file.

However, I have a few questions:
1) how does this plugin deal with sequence GI number? It seems it didn't 
load GI number to SECONDARY_IDENTIFIER on DoTS.ExternalNASequence. For 
example, for AE011191, GI:20520280 is missed.
2) how does this plugin deal with locus_tag? It doesn't load locus_tag 
to SOURCE_ID on all NA feature tables such as DoTS.Transcript.
3) how does this plugin deal with sequence topology?

 

ga GUS::Supported::Plugin::InsertSequenceFeatures 
--mapFile=$GUS_HOME/config/genbank2gus.x
ml --seqFile=/home/data/BRC_genomes/bacillus/AE011191 
--fileFormat=genbank --extDbName=GenBank --extDbRlsVer=138
 --soCvsVersion 1.48 --seqType=DNA --commit
Maximum number of  objects set to 500000
Maximum number of  objects set to 500000
Thu Sep 22 15:10:54 2005        ARGS    algoinvo        1
Thu Sep 22 15:10:54 2005        ARGS    comment
Thu Sep 22 15:10:54 2005        ARGS    commit  1
Thu Sep 22 15:10:54 2005        ARGS    debug   0
Thu Sep 22 15:10:54 2005        ARGS    defaultOrganism
Thu Sep 22 15:10:54 2005        ARGS    description
Thu Sep 22 15:10:54 2005        ARGS    downloadURL
Thu Sep 22 15:10:54 2005        ARGS    extDbName       GenBank
Thu Sep 22 15:10:54 2005        ARGS    extDbRlsDate
Thu Sep 22 15:10:54 2005        ARGS    extDbRlsVer     138
Thu Sep 22 15:10:54 2005        ARGS    failDir
Thu Sep 22 15:10:54 2005        ARGS    fileFormat      genbank
Thu Sep 22 15:10:54 2005        ARGS    filename
Thu Sep 22 15:10:54 2005        ARGS    gff2GroupTag    GenePrediction  Gene
Thu Sep 22 15:10:54 2005        ARGS    gffFormat       2
Thu Sep 22 15:10:54 2005        ARGS    group
Thu Sep 22 15:10:54 2005        ARGS    gusconfigfile   
/home/brcgusts/GUS/gus_home/.gus.properties
Thu Sep 22 15:10:54 2005        ARGS    help
Thu Sep 22 15:10:54 2005        ARGS    helpHTML
Thu Sep 22 15:10:54 2005        ARGS    isUpdateMode    0
Thu Sep 22 15:10:54 2005        ARGS    mapFile 
/home/brcgusts/GUS/gus_home/config/genbank2gus.xml
Thu Sep 22 15:10:54 2005        ARGS    naSequenceSubclass
Thu Sep 22 15:10:54 2005        ARGS    project
Thu Sep 22 15:10:54 2005        ARGS    projectName
Thu Sep 22 15:10:54 2005        ARGS    restartPoint
Thu Sep 22 15:10:54 2005        ARGS    seqFile 
/home/data/BRC_genomes/bacillus/AE011191
Thu Sep 22 15:10:54 2005        ARGS    seqIdColumn     source_id
Thu Sep 22 15:10:54 2005        ARGS    seqSoTerm
Thu Sep 22 15:10:54 2005        ARGS    seqType DNA
Thu Sep 22 15:10:54 2005        ARGS    soCvsVersion    1.48
Thu Sep 22 15:10:54 2005        ARGS    sqlVerbose      0
Thu Sep 22 15:10:54 2005        ARGS    testNumber
Thu Sep 22 15:10:54 2005        ARGS    user
Thu Sep 22 15:10:54 2005        ARGS    verbose 0
Thu Sep 22 15:10:54 2005        ARGS    veryVerbose     0
Thu Sep 22 15:10:54 2005        COMMIT  commit on
Thu Sep 22 15:10:54 2005        ALGINVID        4362
Thu Sep 22 15:11:09 2005        Inserted 100 feature trees
Thu Sep 22 15:11:11 2005        RESULT  Processed: 
/home/data/BRC_genomes/bacillus/AE011191 : genbank
         Seqs Inserted: 1
         Features Inserted: 426
         Feature Trees Inserted: 114

[GUSDEV] schema documentation ( and the plugins), revisited

[Josef J. <ju...@cs...>]

Steve Fischer <sfi...@pc...> writes:
>
> there isn't any parallel document for AAFeatureImp as of yet, that i
> know of.


Then let's start one.  First we need a mapping of
genbank features to gus tables.  Here is the list of
aa feature names from the genbank files I am presently
working with:

  Bond
  CDS
  gene            DoTS::AAGene (** see below)
  Het
  mat_peptide
  proprotein
  Protein
  Region
  SecStr          DoTS::SecondaryStructureAAFeature
  sig_peptide     DoTS::SignalPeptideFeature
  Site
  source          (I assume we don't bother to put this one in a featuretable).

The right side is my guess as to what view on AAFeature that
this particular feature uses.  Ok, I did not get very far.

Can someone help me by filling in the rest?

Also, is the following a complete list of views on DoTS.AAFeatureImp?:

    DoTS::AAFeature
    DoTS::AASeqVariation
    DoTS::DomainFeature
    DoTS::EpitopeFeature
    DoTS::LowComplexityAAFeature
    DoTS::MassSpecFeature
    DoTS::PlasmoAPFeature
    DoTS::PostTranslationalModFeature
    DoTS::PredictedAAFeature
    DoTS::RepeatRegionAAFeature
    DoTS::SecondaryStructureAAFeature
    DoTS::SignalPeptideFeature
    DoTS::TertiaryStructureAAFeature
    DoTS::TranslatedAAFeature

Thank you for your help!

Josef

** Why is DoTS.GeneFeature a view on DoTS.NAFeatureImp though
DoTS.AAGene not a view on DoTS.AAFeature?

Thanks again.

Re: [GUSDEV] schema documentation ( and the plugins), revisited

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

there isn't any parallel document for AAFeatureImp as of yet, that i 
know of.

steve

Josef Jurek wrote:

>I have been working with the InsertSequenceFeatures
>plugin and it has been invaluable towards understanding
>the intended use of the schema.
>
>The provided genbank2gus.xml file is in itself, quite a
>useful piece of schema documentation, however it only
>documents tables which are views on NAFeatureImp.
>
>Is there such a document for views on AAFeatureImp?
>If not, does anyone have similar documentation on
>AAFeature tables?
>
>Thank you for your help;
>
>
>Josef
>
>
>Josef Jurek, Ph.D.
>
>Daphne Preuss Laboratory
>Molecular Genetics and Cell Biology
>The University of Chicago
>ju...@cs...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>
>
>
>
>
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by:
>Tame your development challenges with Apache's Geronimo App Server. 
>Download it for free - -and be entered to win a 42" plasma tv or your very
>own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
>_______________________________________________
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>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>