gusdev-gusdev — Topics concerning GUS development

Re: [GUSDEV] SVN via browser

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

The svn browser has been unavailable since we moved the repository to a new
server.  I hope to have it back up an running shortly.

Thanks,

Mike


On 10/15/05 5:45 PM, "Fabr=EDcio" <fab...@de...> wrote:

> Hello all,
>=20
> =20
>=20
> I=B9ve tried to browse GUS svn using the link in gusdb
> (https://www.cbil.upenn.edu/svnweb/index.cgi/), but the site has an error
> saying that the repository wasn=B9t found. Was it change?
>=20
> =20
>=20
> Regards,
>=20
> =20
>=20
> Fabricio.
>=20

Re: [GUSDEV] A comment to SequenceOntology table

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

This has been fixed in GUS 3.5.1

https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=28

--Mike


On 10/17/05 4:58 PM, "Weichen Wu" <we...@se...> wrote:

> 
> The length of Definition column in SequenceOntology table is 1000. That is
> not enough for the current  so.definition version 1.42. Some of the terms'
> defintions are larger than 1000. For example, term group_II_intron, snoRNA
> and SRP_RNA. Hope the next version will extend the length of this field.
> 
> 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

[GUSDEV] Re: A comment to SequenceOntology table

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

My GUS instance is on Postgresql,  GUS instance on Oracle may not have this 
problem.

Thanks,
Weichen
----- Original Message ----- 
From: "Weichen Wu" <we...@se...>
To: <gus...@li...>
Sent: Monday, October 17, 2005 4:58 PM
Subject: A comment to SequenceOntology table


>
> The length of Definition column in SequenceOntology table is 1000. That is 
> not enough for the current  so.definition version 1.42. Some of the terms' 
> defintions are larger than 1000. For example, term group_II_intron, snoRNA 
> and SRP_RNA. Hope the next version will extend the length of this field.
>
> Thanks,
> Weichen
>
> 

[GUSDEV] A comment to SequenceOntology table

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

The length of Definition column in SequenceOntology table is 1000. That is 
not enough for the current  so.definition version 1.42. Some of the terms' 
defintions are larger than 1000. For example, term group_II_intron, snoRNA 
and SRP_RNA. Hope the next version will extend the length of this field.

Thanks,
Weichen

[GUSDEV] Re: Drop foreign keys to fix InsertGeneOntology pending problem in Postgresql

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

I found it.
alter table sres.goterm drop constraint goterm_fk02;

----- Original Message ----- 
From: "Weichen Wu" <we...@se...>
To: <gus...@li...>
Sent: Monday, October 17, 2005 10:41 AM
Subject: Drop foreign keys to fix InsertGeneOntology pending problem in 
Postgresql


> Hi Mike,
>
> Bug report id=41 suggested to manually drop some foreign keys to solve 
> this bug. Do you remember which foreign keys should be dropped?
>
> Thanks,
> Weichen
>
> 

[GUSDEV] Drop foreign keys to fix InsertGeneOntology pending problem in Postgresql

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

Hi Mike,

Bug report id=41 suggested to manually drop some foreign keys to solve this 
bug. Do you remember which foreign keys should be dropped?

Thanks,
Weichen

[GUSDEV] SVN via browser

[<fab...@de...>]

Hello all,

=20

I=92ve tried to browse GUS svn using the link in gusdb
(https://www.cbil.upenn.edu/svnweb/index.cgi/), but the site has an =
error
saying that the repository wasn=92t found. Was it change?=20

=20

Regards,

=20

Fabricio.

[GUSDEV] GusSchema 3.5.1 Release, Stand-alone SchemaBrowser

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

All,

I'm pleased to announce the release of GusSchema 3.5.1, which is a patch
release with minor changes to the 3.5 schema.  An upgrade script is included
for specific changes and for upgrading from GUS 3.5  Note:  patch releases
are designed to be backwards compatible, so you may upgrade to 3.5.1 without
worry about code compatibility.  Since this is the first release of
GusSchema since being split out from the the GUS package, it will need the
latest install and GUS packages from the repository.

Also, I want to announce the availability of a stand-alone SchemaBrowser,
developed by Conrad Ibanez and collaborators at the University of Georgia.
It is available for download from the GUS website and requires Java 1.5.

The list of items for GusSchema 3.6 is growing; please either send an email
to the list or add an issue to the tracker if you have schema changes you'd
like to raise for the next release.  Also, an update release of
GusAppFramework and install are on the horizon in the coming weeks.

Thanks,

--Mike 

Re: [GUSDEV] LoadTaxon tax_id null error

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

I knew this sounded familiar-- Debbie's post refreshed my memory.  This is
an open issue and there is an entry in the tracker for it:

https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=45

Based on the tracker comments, this error only appears when not in commit
mode.

I've increased the priority in the tracker, and this is scheduled for
resolution in the next release.

--Mike


On 10/11/05 9:04 AM, "pi...@pc..." <pi...@pc...> wrote:

> Merges are updates to the existing db. It occurs when NCBI merges or
> transforms
> one tax_id with another and the merge file is cumulative. If this is the first
> loading of the NCBI taxon, then your db instance will have none of
> these tax id
> to merge and you'll get this message. In the future you will get fewer.
> Therefore, this is OK.
> 
> The failure you get is more serious. Did you provide the entire node.dmp file.
> It looks like you didn't get the taxon table loaded. That must occur before
> loading the taxonname table. One thought, I think you need to load with commit
> on.
> 
>                                                Deborah
> 
> 
> Quoting Weichen Wu <we...@se...>:
> 
>> My GUS 3.5 instance is complete new and I am loading NCBI Taxon data
>> files using LoadTaxon.pm plugin. I have this problem about null value
>> of tax_id. Do I need load anything else before loading taxon?
>> The log is as follows:
>> 
>> [wewu@noodle ncbi_taxon]$     ga GUS::Supported::Plugin::LoadTaxon
>> --nodes nodes.dmp --names names.dmp --gencode gencode.dmp --merged
>> merged.dmp
>> Mon Oct 10 16:37:29 2005        ARGS    algoinvo        1
>> <... skip some lines>
>> Mon Oct 10 16:37:29 2005        Doing merge and NCBI tax id '12' not
>> in database, skipping
>> <...skip many lines>
>> Mon Oct 10 16:37:33 2005        Doing merge and NCBI tax id '349635'
>> not in database, skipping
>> Mon Oct 10 16:37:33 2005        Updating and inserting SRes.GeneticCode
>> Mon Oct 10 16:37:50 2005        Number processed: 1000
>> <...skip many lines>
>> Mon Oct 10 16:54:33 2005        Number processed: 278000
>> Mon Oct 10 16:54:34 2005        Inserting and updating TaxonName
>> 
>> DBD::Pg::st execute failed: ERROR:  null value in column "taxon_id"
>> violates not-null constraint
>> ERROR:
>> SQL ERROR!! involving
>>    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write,
>> other_read, group_read, name, taxon_id, user_read, row_user_id,
>> modification_date, name_class, other_write, row_alg_invocation_id,
>> row_project_id, taxon_name_id, row_group_id, user_write )
>>    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
>> Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1
>> at /home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>> line 166
>> 
>> Thanks,
>> Weichen
>> 
>> 
>> 
>> ----- Original Message ----- From: "Steve Fischer" <sfi...@pc...>
>> To: "Weichen Wu" <we...@se...>
>> Cc: <gus...@li...>
>> Sent: Saturday, October 08, 2005 7:29 AM
>> Subject: Re: [GUSDEV] mapping file
>> 
>> 
>>> yes, the mapping file is required.  you can use the genbank2gus.xml
>>> file if your embl file uses features and qualifiers that conform to
>>> the genbank/embl/ddbj feature table (see
>>> http://www.ncbi.nlm.nih.gov/collab/FT/).
>>> but, you must understand that input often does not conform, or,
>>> places data into qualifiers in the wrong way.
>>> 
>>> in this case, you will need to provide your own mapping file.
>>> 
>>> here is a snip from the documentation from the plugin (i just
>>> improved the doc in latest plugin version):
>>> 
>>> --------
>>> Another way to generate a template mapping file is by using the
>>> command reportFeatureQualifiers.  This command analyzes a set of
>>> input files, and reports the feature/qualifier structure found in
>>> them.  It can output the report in simple text form, or in XML that
>>> is a template for the mapping file.
>>> --------
>>> 
>>> steve
>>> 
>>> Weichen Wu wrote:
>>> 
>>>> Hi,
>>>> 
>>>> To use InsertSequenceFeatures plugin, is the mapping file is
>>>> required? There is a genebank2gus.xml. Is there a mapping file for
>>>> EMBL format available?
>>>> 
>>>> 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
>>> 
>> 
>> 
>> 
>> -------------------------------------------------------
>> 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
>> 
> 
> 
> 
> 
> 
> -------------------------------------------------------
> 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

Re: [GUSDEV] LoadTaxon tax_id null error

[<pi...@pc...>]

Merges are updates to the existing db. It occurs when NCBI merges or 
transforms
one tax_id with another and the merge file is cumulative. If this is the first
loading of the NCBI taxon, then your db instance will have none of 
these tax id
to merge and you'll get this message. In the future you will get fewer.
Therefore, this is OK.

The failure you get is more serious. Did you provide the entire node.dmp file.
It looks like you didn't get the taxon table loaded. That must occur before
loading the taxonname table. One thought, I think you need to load with commit
on.

                                               Deborah


Quoting Weichen Wu <we...@se...>:

> My GUS 3.5 instance is complete new and I am loading NCBI Taxon data 
> files using LoadTaxon.pm plugin. I have this problem about null value 
> of tax_id. Do I need load anything else before loading taxon?
> The log is as follows:
>
> [wewu@noodle ncbi_taxon]$     ga GUS::Supported::Plugin::LoadTaxon 
> --nodes nodes.dmp --names names.dmp --gencode gencode.dmp --merged 
> merged.dmp
> Mon Oct 10 16:37:29 2005        ARGS    algoinvo        1
> <... skip some lines>
> Mon Oct 10 16:37:29 2005        Doing merge and NCBI tax id '12' not 
> in database, skipping
> <...skip many lines>
> Mon Oct 10 16:37:33 2005        Doing merge and NCBI tax id '349635' 
> not in database, skipping
> Mon Oct 10 16:37:33 2005        Updating and inserting SRes.GeneticCode
> Mon Oct 10 16:37:50 2005        Number processed: 1000
> <...skip many lines>
> Mon Oct 10 16:54:33 2005        Number processed: 278000
> Mon Oct 10 16:54:34 2005        Inserting and updating TaxonName
>
> DBD::Pg::st execute failed: ERROR:  null value in column "taxon_id" 
> violates not-null constraint
> ERROR:
> SQL ERROR!! involving
>    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write, 
> other_read, group_read, name, taxon_id, user_read, row_user_id, 
> modification_date, name_class, other_write, row_alg_invocation_id, 
> row_project_id, taxon_name_id, row_group_id, user_write )
>    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
> Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1 
> at /home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm 
> line 166
>
> Thanks,
> Weichen
>
>
>
> ----- Original Message ----- From: "Steve Fischer" <sfi...@pc...>
> To: "Weichen Wu" <we...@se...>
> Cc: <gus...@li...>
> Sent: Saturday, October 08, 2005 7:29 AM
> Subject: Re: [GUSDEV] mapping file
>
>
>> yes, the mapping file is required.  you can use the genbank2gus.xml 
>> file if your embl file uses features and qualifiers that conform to 
>> the genbank/embl/ddbj feature table (see 
>> http://www.ncbi.nlm.nih.gov/collab/FT/).
>> but, you must understand that input often does not conform, or, 
>> places data into qualifiers in the wrong way.
>>
>> in this case, you will need to provide your own mapping file.
>>
>> here is a snip from the documentation from the plugin (i just 
>> improved the doc in latest plugin version):
>>
>> --------
>> Another way to generate a template mapping file is by using the 
>> command reportFeatureQualifiers.  This command analyzes a set of 
>> input files, and reports the feature/qualifier structure found in 
>> them.  It can output the report in simple text form, or in XML that 
>> is a template for the mapping file.
>> --------
>>
>> steve
>>
>> Weichen Wu wrote:
>>
>>> Hi,
>>>
>>> To use InsertSequenceFeatures plugin, is the mapping file is 
>>> required? There is a genebank2gus.xml. Is there a mapping file for 
>>> EMBL format available?
>>>
>>> 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
>>
>
>
>
> -------------------------------------------------------
> 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
>

[GUSDEV] LoadTaxon tax_id null error

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

My GUS 3.5 instance is complete new and I am loading NCBI Taxon data files 
using LoadTaxon.pm plugin. I have this problem about null value of tax_id. 
Do I need load anything else before loading taxon?
The log is as follows:

[wewu@noodle ncbi_taxon]$     ga GUS::Supported::Plugin::LoadTaxon --nodes 
nodes.dmp --names names.dmp --gencode gencode.dmp --merged merged.dmp
Mon Oct 10 16:37:29 2005        ARGS    algoinvo        1
<... skip some lines>
Mon Oct 10 16:37:29 2005        Doing merge and NCBI tax id '12' not in 
database, skipping
<...skip many lines>
Mon Oct 10 16:37:33 2005        Doing merge and NCBI tax id '349635' not in 
database, skipping
Mon Oct 10 16:37:33 2005        Updating and inserting SRes.GeneticCode
Mon Oct 10 16:37:50 2005        Number processed: 1000
<...skip many lines>
Mon Oct 10 16:54:33 2005        Number processed: 278000
Mon Oct 10 16:54:34 2005        Inserting and updating TaxonName

DBD::Pg::st execute failed: ERROR:  null value in column "taxon_id" violates 
not-null constraint
ERROR:
 SQL ERROR!! involving
    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write, 
other_read, group_read, name, taxon_id, user_read, row_user_id, 
modification_date, name_class, other_write, row_alg_invocation_id, 
row_project_id, taxon_name_id, row_group_id, user_write )
    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
 Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1 at 
/home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166

Thanks,
Weichen



----- Original Message ----- 
From: "Steve Fischer" <sfi...@pc...>
To: "Weichen Wu" <we...@se...>
Cc: <gus...@li...>
Sent: Saturday, October 08, 2005 7:29 AM
Subject: Re: [GUSDEV] mapping file


> yes, the mapping file is required.  you can use the genbank2gus.xml file 
> if your embl file uses features and qualifiers that conform to the 
> genbank/embl/ddbj feature table (see 
> http://www.ncbi.nlm.nih.gov/collab/FT/).
> but, you must understand that input often does not conform, or, places 
> data into qualifiers in the wrong way.
>
> in this case, you will need to provide your own mapping file.
>
> here is a snip from the documentation from the plugin (i just improved the 
> doc in latest plugin version):
>
> --------
> Another way to generate a template mapping file is by using the command 
> reportFeatureQualifiers.  This command analyzes a set of input files, and 
> reports the feature/qualifier structure found in them.  It can output the 
> report in simple text form, or in XML that is a template for the mapping 
> file.
> --------
>
> steve
>
> Weichen Wu wrote:
>
>> Hi,
>>
>> To use InsertSequenceFeatures plugin, is the mapping file is required? 
>> There is a genebank2gus.xml. Is there a mapping file for EMBL format 
>> available?
>>
>> 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
> 

[GUSDEV] vacation from 10/7-10/17

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

I'll be unreachable until Tuesday 10/18.

Steve

Re: [GUSDEV] mapping file

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

yes, the mapping file is required.  you can use the genbank2gus.xml file 
if your embl file uses features and qualifiers that conform to the 
genbank/embl/ddbj feature table (see  
http://www.ncbi.nlm.nih.gov/collab/FT/). 

but, you must understand that input often does not conform, or, places 
data into qualifiers in the wrong way.

in this case, you will need to provide your own mapping file.

here is a snip from the documentation from the plugin (i just improved 
the doc in latest plugin version):

--------
Another way to generate a template mapping file is by using the command 
reportFeatureQualifiers.  This command analyzes a set of input files, 
and reports the feature/qualifier structure found in them.  It can 
output the report in simple text form, or in XML that is a template for 
the mapping file.
--------

steve

Weichen Wu wrote:

> Hi,
>
> To use InsertSequenceFeatures plugin, is the mapping file is required? 
> There is a genebank2gus.xml. Is there a mapping file for EMBL format 
> available?
>
> 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

[GUSDEV] mapping file

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

Hi,

To use InsertSequenceFeatures plugin, is the mapping file is required? There 
is a genebank2gus.xml. Is there a mapping file for EMBL format available?

Thanks,
Weichen

Re: [GUSDEV] SVN repos

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

Yes.  You may accept the certificate permanently.

--Mike


On 10/7/05 8:48 AM, "Henrique Juc=E1" <hen...@gm...> wrote:

> Hi all...
>=20
> I've tried to checkout the new repos, but I got a certificate warning:
>=20
> svn checkout https://svn.cbil.upenn.edu/gus
> Error validating server certificate for 'https://svn.cbil.upenn.edu:443':
>  - The certificate is not issued by a trusted authority. Use the
>    fingerprint to validate the certificate manually!
>  - The certificate hostname does not match.
> Certificate information:
>  - Hostname: localhost.localdomain
>  - Valid: from Aug 24 04:25:32 2005 GMT until Aug 24 04:25:32 2006 GMT
>  - Issuer: SomeOrganizationalUnit, SomeOrganization, SomeCity, SomeState,=
 --
>  - Fingerprint: 34:e6:26:36:39:ec:02:75:2e:0c:0e:93:11:54:1a:ac:d0:22:75:=
45
>=20
> Is the repos working fine?
>=20
>=20
> Thanks,
>=20
>=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
> -------------------------------------------------------
> 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

[GUSDEV] SVN repos

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

Hi all...

I've tried to checkout the new repos, but I got a certificate warning:

svn checkout https://svn.cbil.upenn.edu/gus
Error validating server certificate for 'https://svn.cbil.upenn.edu:443':
 - The certificate is not issued by a trusted authority. Use the
   fingerprint to validate the certificate manually!
 - The certificate hostname does not match.
Certificate information:
 - Hostname: localhost.localdomain
 - Valid: from Aug 24 04:25:32 2005 GMT until Aug 24 04:25:32 2006 GMT
 - Issuer: SomeOrganizationalUnit, SomeOrganization, SomeCity, SomeState, -=
-
 - Fingerprint: 34:e6:26:36:39:ec:02:75:2e:0c:0e:93:11:54:1a:ac:d0:22:75:45

Is the repos working fine?


Thanks,




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

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

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] small problem of the plugin version

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

The problem is that the plugin has not been upgraded to conform to the 
3.5 Plugin API.

You will need to read and improve the plugin code.  Compare it to a 
supported plugin.

Which plugin are you using, and what are you attempting to do?

steve

ji...@it... wrote:

>Hello, everyone!
>
>I am a new comer to this group. I look forward to have a good time here.
>
>Recently I met some problem of GUS plugin. I want to reuse some plugin
>designed for GUS 3.0 to the GUS 3.5. But the execution result is shown
>like this way:
>-------------------------------------------------------------
>Database version does not match required version for Plugin.
>Database Version: 3.5    Plugin Version: HASH(0x8132964)
>-------------------------------------------------------------
>
>I did update my modified plugin file to the registery of GUS. But the
>problem can not be solved. The table that I used in my plugin is only
>related with DoTS::NASequence, just 3 simple features. Maybe this is a
>simple problem. But as a novice on GUS, I really require some good advices
>from you. Thank you very much.
>
>
>
>
>
>-------------------------------------------------------
>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
>  
>

[GUSDEV] small problem of the plugin version

[<ji...@it...>]

Hello, everyone!

I am a new comer to this group. I look forward to have a good time here.

Recently I met some problem of GUS plugin. I want to reuse some plugin
designed for GUS 3.0 to the GUS 3.5. But the execution result is shown
like this way:
-------------------------------------------------------------
Database version does not match required version for Plugin.
Database Version: 3.5    Plugin Version: HASH(0x8132964)
-------------------------------------------------------------

I did update my modified plugin file to the registery of GUS. But the
problem can not be solved. The table that I used in my plugin is only
related with DoTS::NASequence, just 3 simple features. Maybe this is a
simple problem. But as a novice on GUS, I really require some good advices
from you. Thank you very much.

[GUSDEV] BioperlFeatMapperSet plugin

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

Hi,

Since the Source Repository is temporary unavailable and the 
BioperlFeatMapperSet plugin is not in 
https://svn.cbil.upenn.edu/gus/GusAppFramework/trunk/Supported/plugin/perl/, 
can I find it somewhere else?

Thanks,
Weichen

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

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

by the way, to get this command, do this:

% cd $PROJECT_HOME/install
% svn update
% rehash  (if you use csh or tcsh)

steve

Steve Fischer wrote:

> this is admitedly a shortcut.
>
> sorry, its all i have time for now.
>
> steve
>
> Michael Saffitz wrote:
>
>> I'm not a big fan of the shortcut command.  If the motivation is that 
>> 90% of
>> the time the command is run as:
>>
>> build proj/comp install -append
>>
>> Then let's change the command so that install -append are the 
>> default, or at
>> least that it can run with abbreviated arguments:
>>
>> build proj i or build proj we
>>
>> Let's fix the underlying problem (poorly designed arguments to build)
>> instead of masking it.  Then, if people still feel it's too long, 
>> they can
>> alias in their shell.
>>
>> --Mike
>>
>>
>>
>> On 10/4/05 4:13 PM, "Y. Thomas Gan" <yon...@pc...> wrote:
>>
>>  
>>
>>> I find it inconvenient/confusing when I have to switch to the full 
>>> command
>>> synopsis if I want to have additional options such as -clean and
>>> -skipJavaCompiling, or if I need to do a webinstall.
>>>
>>> I would argue for making the shortcut to also take other options 
>>> supported
>>> by the full command.
>>>
>>> I guess we could do something for build project/[component] webinstall
>>> too, we can simply use alias instead.
>>>
>>> -Thomas
>>>
>>>
>>> On Tue, 4 Oct 2005, Steve Fischer wrote:
>>>
>>>   
>>>
>>>> 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'
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> 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
>>>>
>>>>     
>>>
>>> -------------------------------------------------------
>>> 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
>>>   
>>
>>
>>  
>>
>
>
> -------------------------------------------------------
> 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

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

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

this is admitedly a shortcut.

sorry, its all i have time for now.

steve

Michael Saffitz wrote:

>I'm not a big fan of the shortcut command.  If the motivation is that 90% of
>the time the command is run as:
>
>build proj/comp install -append
>
>Then let's change the command so that install -append are the default, or at
>least that it can run with abbreviated arguments:
>
>build proj i or build proj we
>
>Let's fix the underlying problem (poorly designed arguments to build)
>instead of masking it.  Then, if people still feel it's too long, they can
>alias in their shell.
>
>--Mike
>
>
>
>On 10/4/05 4:13 PM, "Y. Thomas Gan" <yon...@pc...> wrote:
>
>  
>
>>I find it inconvenient/confusing when I have to switch to the full command
>>synopsis if I want to have additional options such as -clean and
>>-skipJavaCompiling, or if I need to do a webinstall.
>>
>>I would argue for making the shortcut to also take other options supported
>>by the full command.
>>
>>I guess we could do something for build project/[component] webinstall
>>too, we can simply use alias instead.
>>
>>-Thomas
>>
>>
>>On Tue, 4 Oct 2005, Steve Fischer wrote:
>>
>>    
>>
>>>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'
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>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
>>>
>>>      
>>>
>>-------------------------------------------------------
>>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
>>    
>>
>
>  
>

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

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

I'm not a big fan of the shortcut command.  If the motivation is that 90% of
the time the command is run as:

build proj/comp install -append

Then let's change the command so that install -append are the default, or at
least that it can run with abbreviated arguments:

build proj i or build proj we

Let's fix the underlying problem (poorly designed arguments to build)
instead of masking it.  Then, if people still feel it's too long, they can
alias in their shell.

--Mike



On 10/4/05 4:13 PM, "Y. Thomas Gan" <yon...@pc...> wrote:

> I find it inconvenient/confusing when I have to switch to the full command
> synopsis if I want to have additional options such as -clean and
> -skipJavaCompiling, or if I need to do a webinstall.
> 
> I would argue for making the shortcut to also take other options supported
> by the full command.
> 
> I guess we could do something for build project/[component] webinstall
> too, we can simply use alias instead.
> 
> -Thomas
> 
> 
> On Tue, 4 Oct 2005, Steve Fischer wrote:
> 
>> 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'
>> 
>> 
>> 
>> -------------------------------------------------------
>> 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
>> 
> 
> 
> -------------------------------------------------------
> 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

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

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

I find it inconvenient/confusing when I have to switch to the full command 
synopsis if I want to have additional options such as -clean and 
-skipJavaCompiling, or if I need to do a webinstall.

I would argue for making the shortcut to also take other options supported 
by the full command.

I guess we could do something for build project/[component] webinstall 
too, we can simply use alias instead.

-Thomas


On Tue, 4 Oct 2005, Steve Fischer wrote:

> 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'
>
>
>
> -------------------------------------------------------
> 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
>

Re: [GUSDEV] ** Repository Move Complete

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

See comments below.

On 10/4/05 1:28 PM, "Chris Topinka" <cmt...@gm...> wrote:

> Greetings,
> 
> How exactly is the repository administrated?

The repository is administered by CBIL, who hosts the project on behalf of
the GUS community.

> How are you adding contributors to the development team. If I start writing
> plug-ins or altering code in the application layer or altering the schema how
> do I know if someone else isn't working on the same or similar functionality?

The best thing to do here is email the list with an outline of what you're
working on and your thoughts.  This way, others will know what's going on,
and you can collaborate as appropriate.  If you don't already have commit
access, it will also be granted as needed upon request.

> If we wanted to become
> developers how would our contributions be reviewed?

All commits are reviewed through the commits mailing list, but it's an
informal process.  Basically, the only thing I can anticipate being refused
is either very poor code or a niche need that has negative side effects for
the community.

> Have other groups had
> problems with locally altering the project in a way that suits their needs
> and then becoming out of sync or breaking the CVS version?

I'm not sure about this, but I doubt it.  I don't think anyone has
significantly altered the code locally.

Are you identifying areas that don't meet your needs?  Perhaps you can
highlight some of your findings in evaluating GUS to the community, and we
can provide feedback and coordinate or points for collaboration.

Thanks,

Mike

> 
> Thanks,
> 
> Chris Topinka
> 
> On 10/4/05, Michael Saffitz <msa...@pc...> wrote:
>> 
>> 
>> 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.
>> 
>> 
>> 
>> 
>> -------------------------------------------------------
>> 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
>> 
> 
> 
> 
> --
> Christopher M. Topinka
> NLM-BHIRT Predoctoral Fellow in Computer Science
> 113 Life Sciences Center
> University of Missouri
> Columbia, MO 65211
> (573)-823-0616
> cmt...@mi...

Re: [GUSDEV] ** Repository Move Complete

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

Greetings,

How exactly is the repository administrated? How are you adding contributor=
s
to the development team. If I start writing plug-ins or altering code in th=
e
application layer or altering the schema how do I know if someone else isn'=
t
working on the same or similar functionality? If we wanted to become
developers how would our contributions be reviewed? Have other groups had
problems with locally altering the project in a way that suits their needs
and then becoming out of sync or breaking the CVS version?

Thanks,

Chris Topinka

On 10/4/05, Michael Saffitz <msa...@pc...> wrote:
>
>
> 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.
>
>
>
>
> -------------------------------------------------------
> 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
>



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