gusdev-gusdev — Topics concerning GUS development

RE: [GUSDEV] WDK installation error

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

We just ran wdkTestDb here against a postgres database without a
problem.

Please check your $GUS_HOME/data/WDKToySite/Model/testTables/WDKTestEst
The first line of that file should specify datatypes for each column,
first of which should say "row_project_id number(10) not null".
The first column of all lines that follow should be numeric (10 to be
specific).

If there is no unexpected problem there, then make sure you start your
WDK installation with clean (no old code)
and dedicated (no code from other projects, especially GUS)
$PROJECT_HOME and $GUS_HOME

-Thomas

> -----Original Message-----
> From: gus...@li...=20
> [mailto:gus...@li...] On Behalf=20
> Of Y. Thomas Gan
> Sent: Wednesday, March 08, 2006 10:29 AM
> To: 'Henrique Juc?; 'Gusdev gusdev-gusdev'
> Subject: RE: [GUSDEV] WDK installation error
>=20
>=20
> Dear Henrigue,
> WDK has been tested and used mostly with oracle databases so=20
> it is possible that you are hitting a postgres specific WDK=20
> bug. We will see if we can reproduce the behavior here and=20
> get back to you. If would be helpful if you could let us know=20
> what version of WDK you are using.=20
>=20
> Have you run wdkCache command yet? If not can you run it to=20
> see if you can successfully create the cache tables needed by WDK?
>=20
> -Thomas
>=20
> -----Original Message-----
> From: gus...@li...
> [mailto:gus...@li...] On Behalf=20
> Of Henrique Juc
> Sent: Tuesday, March 07, 2006 1:38 PM
> To: Gusdev gusdev-gusdev
> Subject: [GUSDEV] WDK installation error
>=20
>=20
> Hi everyone,
>=20
> I'm trying to install WDK to use along with GUS, however I'm=20
> getting the following error. I'm using the files provided=20
> with the WDK package. The error is the following:
>=20
> [juca1@kineto3 config]$ wdkTestDb -model toyModel -create
> Table usertest.WDKTestEst already exists; no change made.  To=20
> reload this table, first drop it and then create it again=20
> Loading table usertest.WDKTestTaxonName to database from file
>=20
> ERROR: column "row_project_id" is of type numeric but=20
> expression is of type character varying
> java.sql.SQLException: ERROR: column "row_project_id" is of=20
> type numeric but expression is of type character varying
>         at org.postgresql.core.v3.QueryExe=20
> cutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1471)
>         at=20
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryE
> xecutorImp
> l.java:1256)
>         at
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutor
> Impl.java:
> 175)
>         at=20
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJd
> bc2Stateme
> nt.java:392)
>         at=20
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(A
> bstractJdb
> c2Statement.java:330)
>         at=20
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(Abst
> ractJdbc2S
> tatement.java:282)
>         at=20
> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpd
> ate(Delega
> tingPreparedStatement.java:233)
>         at=20
> org.gusdb.wdk.model.implementation.SqlUtils.getResultSet(SqlUt
> ils.java:5
> 1)
>         at
> org.gusdb.wdk.model.test.TestDBManager.main(TestDBManager.java:117)
>=20
> The first part I understand as the tables were already there,=20
> but that seems not to be part of the problem, as I dropped=20
> the tables, but the problem persisted. What should I do? Any=20
> suggestions?
>=20
> Thanks in advance,
>=20
>=20
> Henrique Cesar Lemos Juc=E1=20
> Bi=F3logo/Tecnologista - FAPERJ
>=20
http://www.biowebdb.org
http://www.bioinformatica.ufsc.br


"As soon as you concern yourself with the "good" and "bad" of your
fellows,=20
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



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RE: [GUSDEV] WDK installation error

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

Dear Henrigue,
WDK has been tested and used mostly with oracle databases so it is
possible that you are hitting a postgres specific WDK bug.
We will see if we can reproduce the behavior here and get back to you.
If would be helpful if you could let us know what version of WDK you are
using.=20

Have you run wdkCache command yet? If not can you run it to see if you
can successfully create the cache tables needed by WDK?

-Thomas

-----Original Message-----
From: gus...@li...
[mailto:gus...@li...] On Behalf Of Henrique
Juc
Sent: Tuesday, March 07, 2006 1:38 PM
To: Gusdev gusdev-gusdev
Subject: [GUSDEV] WDK installation error


Hi everyone,

I'm trying to install WDK to use along with GUS, however I'm getting the
following error. I'm using the files provided with the WDK package. The
error is the following:

[juca1@kineto3 config]$ wdkTestDb -model toyModel -create
Table usertest.WDKTestEst already exists; no change made.  To reload
this table, first drop it and then create it again
Loading table usertest.WDKTestTaxonName to database from file

ERROR: column "row_project_id" is of type numeric but expression is of
type character varying
java.sql.SQLException: ERROR: column "row_project_id" is of type numeric
but expression is of type character varying
        at org.postgresql.core.v3.QueryExe=20
cutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1471)
        at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImp
l.java:1256)
        at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:
175)
        at
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Stateme
nt.java:392)
        at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdb
c2Statement.java:330)
        at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2S
tatement.java:282)
        at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delega
tingPreparedStatement.java:233)
        at
org.gusdb.wdk.model.implementation.SqlUtils.getResultSet(SqlUtils.java:5
1)
        at
org.gusdb.wdk.model.test.TestDBManager.main(TestDBManager.java:117)

The first part I understand as the tables were already there, but that
seems not to be part of the problem, as I dropped the tables, but the
problem persisted. What should I do? Any suggestions?

Thanks in advance,


Henrique Cesar Lemos Juc=E1=20
Bi=F3logo/Tecnologista - FAPERJ

http://www.biowebdb.org
http://www.bioinformatica.ufsc.br


"As soon as you concern yourself with the "good" and "bad" of your
fellows,=20
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

[GUSDEV] [Slightly-OT] ASM with Oracle10G

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

Up to now, we at the Preuss lab have installed and used
GUS under Oracle9i only.  As we are beginning to install
Oracle on a new machine (RHEL ES release 4/Linux 2.6.9-22.ELsmp),
we decided to go with version 10g here.  So far, the only issue
with this installation has been installing the Automatic Storage
System or ASM, a new feature to Oracle10g.

Some questions:

   Is it worth going to ASM instead of just using the 9i
   method of managing tablespaces, what the manual calls the
   "File System" approach?  I suppose I could just
   start with the File System approach and upgrade to ASM
   later.

   ASM Support Library; the manual calls it "optional" yet
   "recommended".  Do people find this worth having?
   As far as I can tell, using the ASMLib means that you cannot
   run SELinux (Security-Enhanced Linux).  Is this what
   other people are finding?

   Our Linux box already has RAID disks, therefore the manual
   seems to indicate that the "external redundancy" option for
   ASM is a way to go as opposed to the "normal redundancy"
   or "high redundancy" options.  Do people agree?

   Does anyone have any suggestions for other things to
   watch out for?

Thanks; Josef



Josef Jurek

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 702-9559
fax:   (773) 702-6648

Re: [GUSDEV] Sugestion for the ISF plugin

[chris m. <cj...@fr...>]

You can increase the threshold at which the severity of a problem 
causes the unflattener to throw an error.

$unf->error_threshold(2);  # do not throw for problems of severity <2

see the docs for more details

The policy here is up to you. As we discovered the last time this came 
up, this particular genbank record has an inconsistency. It's up to you 
whether you want to load the exons from this file, or if you would 
prefer to reject the entire record



On Mar 7, 2006, at 10:36 AM, Steve Fischer wrote:

> in this case, i am not sure this is possible.  the problem is during 
> the bioperl parsing.   if you would like to do the work to investigate 
> whether the bioperl parser (and the unflattener) have options for 
> this, that would be a first step.
>
> steve
>
> Ricardo Balbi wrote:
>
>> Hi all,
>>
>>   Ahead of all the problems that we are facing to load a GenBank file 
>> using the InsertSequenceFeatures (we thougth in coming back to use 
>> the GBParser), we have one sugestion:
>>   Maybe modify the ISF to separate the GIs that present problems in 
>> separate files, as GBParser does, not interrupting the execution.  We 
>> believe that this could help solve many of the problems that we are 
>> finding (and I believe that other groups too) and would very easy to 
>> correct these problems without interrupting the work that we are 
>> carrying at the moment.   We believe that with this modification, the 
>> ISF would become much more flexible and easy to work.
>>
>> thanks in advance,
>> Ricardo
>

[GUSDEV] WDK installation error

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

Hi everyone,

I'm trying to install WDK to use along with GUS, however I'm getting the
following error. I'm using the files provided with the WDK package. The
error is the following:

[juca1@kineto3 config]$ wdkTestDb -model toyModel -create
Table usertest.WDKTestEst already exists; no change made.  To reload this
table, first drop it and then create it again
Loading table usertest.WDKTestTaxonName to database from file

ERROR: column "row_project_id" is of type numeric but expression is of type
character varying
java.sql.SQLException: ERROR: column "row_project_id" is of type numeric bu=
t
expression is of type character varying
        at org.postgresql.core.v3.QueryExe cutorImpl.receiveErrorResponse(
QueryExecutorImpl.java:1471)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(
QueryExecutorImpl.java:1256)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(
QueryExecutorImpl.java:175)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(
AbstractJdbc2Statement.java:392)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(
AbstractJdbc2Statement.java:330)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(
AbstractJdbc2Statement.java:282)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdat=
e
(DelegatingPreparedStatement.java:233)
        at org.gusdb.wdk.model.implementation.SqlUtils.getResultSet(
SqlUtils.java:51)
        at org.gusdb.wdk.model.test.TestDBManager.main(TestDBManager.java
:117)

The first part I understand as the tables were already there, but that seem=
s
not to be part of the problem, as I dropped the tables, but the problem
persisted. What should I do? Any suggestions?

Thanks in advance,


Henrique Cesar Lemos Juc=E1
Bi=F3logo/Tecnologista - FAPERJ

http://www.biowebdb.org
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] Sugestion for the ISF plugin

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

in this case, i am not sure this is possible.  the problem is during the 
bioperl parsing.   if you would like to do the work to investigate 
whether the bioperl parser (and the unflattener) have options for this, 
that would be a first step.

steve

Ricardo Balbi wrote:

> Hi all,
>
>   Ahead of all the problems that we are facing to load a GenBank file 
> using the InsertSequenceFeatures (we thougth in coming back to use the 
> GBParser), we have one sugestion:
>   Maybe modify the ISF to separate the GIs that present problems in 
> separate files, as GBParser does, not interrupting the execution.  We 
> believe that this could help solve many of the problems that we are 
> finding (and I believe that other groups too) and would very easy to 
> correct these problems without interrupting the work that we are 
> carrying at the moment. 
>   We believe that with this modification, the ISF would become much 
> more flexible and easy to work.
>
> thanks in advance,
> Ricardo

Re: [GUSDEV] Re: ISF errors list

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

ISF does not now support any way to ignore a GI. 

so, for now, copy the genbank to file to a .fixed version, and fix the 
problem, either by removing the GI or by tweeking the feaatures

steve

Ricardo Balbi wrote:

> Ok Aaron, but what we have to do ? edit the GenBank file? ignore this 
> GI? if yes, how to ignore?
>
> On 2/16/06, *Aaron J. Mackey* < am...@pc... 
> <mailto:am...@pc...>> wrote:
>
>
>
>     On Feb 17, 2006, at 6:58 PM, davila wrote:
>
>     > 3. 102829.txt - Apparently a BioPerl error
>     > A 102829.gb <http://102829.gb> file is an example
>
>     Read the error message, it tells you exactly what is wrong:
>
>     ------------- EXCEPTION  -------------
>     MSG: 1 there is a conflict with exons; there was an explicitly stated
>     exon with location 12..21, yet I cannot generate this e
>     xon from the supplied mRNA locations
>     1 There are some inferred exons that are not in the explicit exon
>     list; they are the exons at locations:
>     25..447
>
>     STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/lib/
>     perl5/site_perl/5.8.6/Bio/SeqFeature/Tools/Unflattener.pm:1
>     606
>     ...
>
>
>     Then look at the GenBank file:
>
>           gene            1..447
>                           /gene="ESAG1"
>           primer_bind     1..11
>                           /gene="ESAG1"
>           exon            <12..21
>                           /gene="ESAG1"
>                           /note="min-exon"
>           CDS             25..>447
>                           /gene="ESAG1"
>
>     I have to agree with the Unflattener, this doesn't make any sense at
>     all.
>
>     Garbage in, garbage out.
>
>     -Aaron
>
>
>     --
>     Aaron J. Mackey, Ph.D.
>     Project Manager, ApiDB Bioinformatics Resource Center
>     Penn Genomics Institute, University of Pennsylvania
>     email:   am...@pc... <mailto:am...@pc...>
>     office: 215-898-1205 (Biology, 212 Goddard Labs)
>              215-746-7018 (PCBI, 1428 Blockley Hall)
>     fax:    215-746-6697 (Penn Genomics Institute)
>     postal: Penn Genomics Institute
>              Goddard Labs 212
>              415 S. University Avenue
>              Philadelphia, PA  19104-6017
>
>
>
>
>     -------------------------------------------------------
>     This SF.net email is sponsored by: Splunk Inc. Do you grep through
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>
>

[GUSDEV] Sugestion for the ISF plugin

[Ricardo B. <rb...@gm...>]

Hi all,

  Ahead of all the problems that we are facing to load a GenBank file using
the InsertSequenceFeatures (we thougth in coming back to use the GBParser),
we have one sugestion:
  Maybe modify the ISF to separate the GIs that present problems in separat=
e
files, as GBParser does, not interrupting the execution.  We believe that
this could help solve many of the problems that we are finding (and I
believe that other groups too) and would very easy to correct these problem=
s
without interrupting the work that we are carrying at the moment.
  We believe that with this modification, the ISF would become much more
flexible and easy to work.

thanks in advance,
Ricardo

Re: [GUSDEV] Re: ISF errors list

[Ricardo B. <rb...@gm...>]

Ok Aaron, but what we have to do ? edit the GenBank file? ignore this GI? i=
f
yes, how to ignore?

On 2/16/06, Aaron J. Mackey <am...@pc...> wrote:
>
>
>
> On Feb 17, 2006, at 6:58 PM, davila wrote:
>
> > 3. 102829.txt - Apparently a BioPerl error
> > A 102829.gb file is an example
>
> Read the error message, it tells you exactly what is wrong:
>
> ------------- EXCEPTION  -------------
> MSG: 1 there is a conflict with exons; there was an explicitly stated
> exon with location 12..21, yet I cannot generate this e
> xon from the supplied mRNA locations
> 1 There are some inferred exons that are not in the explicit exon
> list; they are the exons at locations:
> 25..447
>
> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/lib/
> perl5/site_perl/5.8.6/Bio/SeqFeature/Tools/Unflattener.pm:1
> 606
> ...
>
>
> Then look at the GenBank file:
>
>       gene            1..447
>                       /gene=3D"ESAG1"
>       primer_bind     1..11
>                       /gene=3D"ESAG1"
>       exon            <12..21
>                       /gene=3D"ESAG1"
>                       /note=3D"min-exon"
>       CDS             25..>447
>                       /gene=3D"ESAG1"
>
> I have to agree with the Unflattener, this doesn't make any sense at
> all.
>
> Garbage in, garbage out.
>
> -Aaron
>
>
> --
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Biology, 212 Goddard Labs)
>          215-746-7018 (PCBI, 1428 Blockley Hall)
> fax:    215-746-6697 (Penn Genomics Institute)
> postal: Penn Genomics Institute
>          Goddard Labs 212
>          415 S. University Avenue
>          Philadelphia, PA  19104-6017
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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=3D121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] Re: ISF errors list

[Ricardo B. <rb...@gm...>]

Hi Aaron,
  This problem still continue ... :(
  We are using BioPerl 1.5.1 and ISF with CVS revision 4573.

  Have you been tried to run ISF with those files sent to the list ?
  Do you have any other tips to us ?

Ricardo

On 2/16/06, Aaron J. Mackey <am...@pc...> wrote:
>
>
> On Feb 17, 2006, at 6:58 PM, davila wrote:
>
> > 2. MSG: operator "gap" unrecognized by parser
> > An gap.tar.gz file was created ana annexed containing several GIs
> > associated to this error.
>
> This is a known (old) BioPerl error; GenBank has introduced/allowed a
> feature location operation called "gap()" (like "join()" or
> "complement()") that is not valid EMBL/GenBank/DDBJ feature-table
> syntax.  See:
>
>    http://bugzilla.open-bio.org/show_bug.cgi?id=3D1319
>
> This is fixed in BioPerl 1.5.1, I believe, and maybe even in 1.4
>
> -Aaron
>
> --
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Biology, 212 Goddard Labs)
>          215-746-7018 (PCBI, 1428 Blockley Hall)
> fax:    215-746-6697 (Penn Genomics Institute)
> postal: Penn Genomics Institute
>          Goddard Labs 212
>          415 S. University Avenue
>          Philadelphia, PA  19104-6017
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=
=3D121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] Newbie Question: GUS on a small scale...

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

john-

yes, that is a good idea.  but, doing that would take a lot of work, 
more than we ourselves have resources for.

in a sense, GUS, as it stands now, is targeted for larger projects.

steve

Fow...@ep... wrote:

>
> Hello,
>
> I apologize if this is not the correct place to post this question/idea.
>
> Briefly, I am a plant molecular biologist that is trying to pick up 
> some rudimentary bioinformatics (eg, relational databases, scripting, 
> etc.)
>
> I would like to build a small-scale database that stores and 
> integrates information on a small number of gene families.  These 
> families are of interest in my lab's various research projects.  The 
> information would be gathered from a few sites on the web, or from 
> manual input (my lab, potentially others).
>
> While looking and reading around, I found the GUS home site, and have 
> browsed through it a bit.
>
> As a newcomer to this field, I confess some ignorance, but have a 
> possible suggestion/idea and question.
>
> My observation is that the information that I'd like to store in the 
> database I am conceiving would all fit in the tables/categories that 
> are present in your schema.  However, I don't think that I would ever 
> need all of the complexity that you have available.
>
> Would it be possible, or recommendable, to develop a smaller, limited 
> set of tables/categories that is derived from GUS for my application? 
>  I am even thinking that it might be useful to develop this smaller 
> schema as a template for a purchased desktop type of database 
> (Filemaker Pro is what I am familiar with), such that 
> non-bioinformatics folks like me could relatively easily develop & 
> maintain lab-specific, small-scale databases.
>
> However, by deriving this schema from your GUS (as a standard) might 
> help allow easier eventual expansion or communication of information.
>
> please provide criticism, or other thoughts.  Is there already 
> something like what I am describing?
>
> many thanks,
> John
>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> John E. Fowler
> Associate Professor, OSU Botany and Plant Pathology Dept.
> On Sabbatical at the EPA Western Ecology Division, Corvallis
> email:  fow...@ep...
> Phone: (541) 754-4866 

[GUSDEV] Newbie Question: GUS on a small scale...

[<Fow...@ep...>]

Hello,

I apologize if this is not the correct place to post this question/idea.

Briefly, I am a plant molecular biologist that is trying to pick up some 
rudimentary bioinformatics (eg, relational databases, scripting, etc.)

I would like to build a small-scale database that stores and integrates 
information on a small number of gene families.  These families are of 
interest in my lab's various research projects.  The information would be 
gathered from a few sites on the web, or from manual input (my lab, 
potentially others).

While looking and reading around, I found the GUS home site, and have 
browsed through it a bit.

As a newcomer to this field, I confess some ignorance, but have a possible 
suggestion/idea and question.

My observation is that the information that I'd like to store in the 
database I am conceiving would all fit in the tables/categories that are 
present in your schema.  However, I don't think that I would ever need all 
of the complexity that you have available.

Would it be possible, or recommendable, to develop a smaller, limited set 
of tables/categories that is derived from GUS for my application?  I am 
even thinking that it might be useful to develop this smaller schema as a 
template for a purchased desktop type of database (Filemaker Pro is what I 
am familiar with), such that non-bioinformatics folks like me could 
relatively easily develop & maintain lab-specific, small-scale databases.

However, by deriving this schema from your GUS (as a standard) might help 
allow easier eventual expansion or communication of information.

please provide criticism, or other thoughts.  Is there already something 
like what I am describing?

many thanks,
John

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
John E. Fowler
Associate Professor, OSU Botany and Plant Pathology Dept.
On Sabbatical at the EPA Western Ecology Division, Corvallis
email:  fow...@ep...
Phone: (541) 754-4866

Re: [GUSDEV] how do we interact with the JAVA objects API layer

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

Hi Dhivya,
Here are the last two recorded entries in the SVN log of the
ObjRelJ/src/java/org/gusdb/objrelj/ directory:

$ svn log  src/java/org/gusdb/objrelj               
------------------------------------------------------------------------
r3115 | msaffitz | 2005-07-18 12:18:39 -0400 (Mon, 18 Jul 2005) | 2 lines
renaming to distinguish from the gus schema project

------------------------------------------------------------------------
r1992 | dbarkan | 2004-05-06 16:33:33 -0400 (Thu, 06 May 2004) | 2 lines
major debugging effort since last commit

ObjeRelJ probably works just fine, but as you can see the last real work 
on this may have been way back in May 2004. Hence the cricket sounds in 
answer to your last email. You will probably need to look through the 
source for your answers.
Personally I use custom Spring + Hibernate code to access the DB w/ 
java, but this does not do the work of GusApplication for insertion into 
Core.ApplicationInvocation, etc., and is no better (probably worse) than 
the WDK for query, but we wanted to keep the same arch & design 
throughout a website that needs to insert on occasion, so no WDK for us.

Good luck!
Angel


Dhivya Aras wrote:

> Hi everyone,
>  
> I've found that while there is a lot of documentation on the schemas 
> of gus, there's not much information about the java API out there. I 
> would like to add new objects to the Java API layer, and so would like 
> to know any information about how to interact with GUS's API layer.
>  
> I would really appreciate some help here.
> thanks
> dhivya
>
> ------------------------------------------------------------------------
> Yahoo! Mail
> Use Photomail 
> <http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=38867/*http://photomail.mail.yahoo.com> 
> to share photos without annoying attachments. 

Re: [GUSDEV] how do we interact with the JAVA objects API layer

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

Hi Dhivya,
Sorry not to respond to your earlier mail. We haven't done a whole  
lot in my group with the Java layer. I think the folks in the Penn  
Bioinformatics Core have used it. Perhaps they can respond? We were  
looking at having the Java objects automatically generated with  
Hibernate.

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 Feb 20, 2006, at 3:20 PM, Dhivya Aras wrote:

> Hi everyone,
>
> I've found that while there is a lot of documentation on the  
> schemas of gus, there's not much information about the java API out  
> there. I would like to add new objects to the Java API layer, and  
> so would like to know any information about how to interact with  
> GUS's API layer.
>
> I would really appreciate some help here.
> thanks
> dhivya
>
> Yahoo! Mail
> Use Photomail to share photos without annoying attachments.

[GUSDEV] how do we interact with the JAVA objects API layer

[Dhivya A. <dhi...@ya...>]

Hi everyone,
   
  I've found that while there is a lot of documentation on the schemas of gus, there's not much information about the java API out there. I would like to add new objects to the Java API layer, and so would like to know any information about how to interact with GUS's API layer.
   
  I would really appreciate some help here.
  thanks
  dhivya

		
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[GUSDEV] Problem installing GUS: " Null version, skipping.", then notdefyet

[Thomas K. <ka...@ip...>]

Hi all,

I cannot install GUS here. First, the schema installation says (complete 
output at the end):

[InstallSchema] 19:20:52,417 ERROR InstallSchemaTask:113 - Null version, 
skipping.  Note:  You will need to manually add a version number to the DB

The installation continues, but aborts soon after with

[javac] 
/home/kappler/rest/software/GUS_svn/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:86: 
cannot find symbol
[javac] symbol  : class notdefyet
[javac] location: class org.gusdb.model.Core.Algorithm_Row
[javac]     public void setModificationDate (notdefyet value)

The DB looks reasonable. core.tableinfo is present and
select modification_date from core.tableinfo;
shows 962 rows contaiing a date from installation time.

What "version number" am I supposed to add to the DB?

I tried both with GUS 3.5.0 and an SVN checkout from today.
Other software used: postgres 8.1.3, java 1.5.0_05, ant 1.6.2.


Regards,
Thomas Kappler

---------
The complete output (only the first two of the javac errors) is:

      [echo]  proj=GUS
      [echo] .
      [echo] Installing CBIL/Bio
      [echo] .
      [echo] Installing CBIL/CSP
      [echo] .
      [echo] Installing CBIL/Util
      [echo] .
      [echo] Installing CBIL/Cider
      [echo] .
      [echo] Installing CBIL/HQ
      [echo] .
      [echo] Installing CBIL/ObjectMapper
    [concat] No existing files and no nested text, doing nothing
      [echo] .
      [echo] Installing GUS/Supported
      [echo] .
      [echo] Installing GUS/Community
      [echo] .
      [echo] Installing GUS/DBAdmin
      [echo] .
      [echo] Installing GUS/GOPredict
      [echo] .
      [echo] Installing GusSchema/Definition
      [echo] .
      [echo] Installing GUS/DBAdmin
[InstallSchema] 19:16:59,480  INFO InstallSchemaTask:73 - Reading 
database from 
/home/kappler/rest/software/GUS_svn/GUS/project_home/GusSchema/Definition/config/gus_schema.xml
[InstallSchema] 19:16:59,578  INFO SchemaReader:48 - Reading Database
[InstallSchema] 19:17:04,504  INFO Database:161 - Resolving Database 
References
[InstallSchema] 19:17:05,467  INFO DatabaseValidator:57 - Validating 
Database: 'null'
[InstallSchema] 19:17:06,083  INFO DatabaseValidator:57 - Validating 
Database: 'null'
[InstallSchema] 19:17:06,130  INFO SchemaWriter:33 - Writing Database
[InstallSchema] 19:17:06,912  INFO DatabaseValidator:57 - Validating 
Database: 'null'
[InstallSchema] 19:17:06,958  INFO SchemaWriter:33 - Writing Database
[InstallSchema] 19:20:19,371 ERROR InstallSchemaTask:113 - Null version, 
skipping.  Note:  You will need to manually add a version number to the DB
[InstallSchema] 19:20:52,417 ERROR InstallSchemaTask:113 - Null version, 
skipping.  Note:  You will need to manually add a version number to the DB
    [concat] No existing files and no nested text, doing nothing
      [echo] .
      [echo] Installing GUS/ObjRelP
      [echo] .
      [echo] Installing GUS/ObjRelJ
      [copy] Copying 2 files to 
/home/kappler/rest/software/GUS_svn/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS
      [copy] Copying 1 file to 
/home/kappler/rest/software/GUS_svn/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes
      [echo] Starting target: JavaModel
      [echo] .
      [echo] Installing GUS/Model
     [javac] Compiling 1281 source files to 
/home/kappler/rest/software/GUS_svn/GUS/project_home/GUS/Model/classlog
     [javac] 
/home/kappler/rest/software/GUS_svn/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:86: 
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/kappler/rest/software/GUS_svn/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:91: 
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"); }
[...]

[GUSDEV] how to add java classes and objects to the java object layer

[Dhivya A. <dhi...@ya...>]

Hi everyone,
   
  I'm trying to add a new schema to GUS, using the biopax data model as reference. I've found tools which convert this data model which is in OWL format into java classes, interfaces and listeners. I know that GUS has a java object layer. I would like to know how to integrate the Java objects created out of Bipax into GUS's java object layer. How do I go about doing that? 
   
  thanks
  dhivya arasappan

			
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[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 1. Can't locate object method "organelle" via
> package"GUS::Supported::SpecialCaseQualifierHandlers".


Does your mapping file provide an entry for the "organelle" tag?  If  
so, it's pointing to the default special case handler, which has no  
ability to handle the "organelle" tag; you'll need to specify your  
own handler if you want to capture the contents of this tag.

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
         215-746-7018 (PCBI, 1428 Blockley Hall)
fax:    215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

I've patched ISF to correct for this misbehavior.  The patch is  
listed below.

-Aaron

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 5. 98198.txt
> It did not find the name of the table taxonomy (the taxonomy table  
> was updated but the error persist)
> The 98198.gb is an example

Index: InsertSequenceFeatures.pm
===================================================================
--- InsertSequenceFeatures.pm   (revision 4572)
+++ InsertSequenceFeatures.pm   (working copy)
@@ -872,14 +872,18 @@
    my $species = $bioperlSeq->species();
    my $sciName;
    if ($species) {
-    $sciName = $species->genus() . " " . $species->species();
+    # for exotic taxa, common name is more likely to match in NCBI
+    # Taxonomy than whatever BioPerl guesses the genus/species names
+    # to be:
+    $sciName = $species->common_name();
    } else {
      $sciName = $self->getArg('defaultOrganism');
      if (!$sciName) {
        my $acc = $bioperlSeq->accession_number();
        $self->userError("Sequence '$acc' does not have organism  
information, and, you have not supplied a --defaultOrganism argument  
on the command line");
      }
-    $sciName =~ /\w+ \w+/ || $self->userError("Command line argument  
'--defaultOrganism $sciName' is not in 'genus species' format");
+    # this is an invalid assumption, e.g. 'Blastocrithidia sp. ex  
Triatoma garciabesi':
+    # $sciName =~ /\w+ \w+/ || $self->userError("Command line  
argument '--defaultOrganism $sciName' is not in 'genus species'  
format");
    }
    return $self->getIdFromCache('taxonNameCache',

[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 4. 64524.txt
> The file 64524.gb is another example


The error is:

Feature 'CDS' has more than one value for tag 'EC_number'
The values are:
         1.2.3.4
         1.6.5.5


The ISF plugin works with a mapping file that either specifies one-to- 
one mappings between feature tags and table columns, or a special  
case handler that will be invoked.  In this case, you have more than  
one EC number, and thus you cannot use a one-to-one mapping (which  
column does your mapping file specify should be used for the EC number?)

GUS does have support for multiple EC#'s per sequence, but you'll  
have to author a special case handler to make use of these tables.

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
         215-746-7018 (PCBI, 1428 Blockley Hall)
fax:    215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 3. 102829.txt - Apparently a BioPerl error
> A 102829.gb file is an example

Read the error message, it tells you exactly what is wrong:

------------- EXCEPTION  -------------
MSG: 1 there is a conflict with exons; there was an explicitly stated  
exon with location 12..21, yet I cannot generate this e
xon from the supplied mRNA locations
1 There are some inferred exons that are not in the explicit exon  
list; they are the exons at locations:
25..447

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/lib/ 
perl5/site_perl/5.8.6/Bio/SeqFeature/Tools/Unflattener.pm:1
606
...


Then look at the GenBank file:

      gene            1..447
                      /gene="ESAG1"
      primer_bind     1..11
                      /gene="ESAG1"
      exon            <12..21
                      /gene="ESAG1"
                      /note="min-exon"
      CDS             25..>447
                      /gene="ESAG1"

I have to agree with the Unflattener, this doesn't make any sense at  
all.

Garbage in, garbage out.

-Aaron


--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
         215-746-7018 (PCBI, 1428 Blockley Hall)
fax:    215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 2. MSG: operator "gap" unrecognized by parser
> An gap.tar.gz file was created ana annexed containing several GIs  
> associated to this error.

This is a known (old) BioPerl error; GenBank has introduced/allowed a  
feature location operation called "gap()" (like "join()" or  
"complement()") that is not valid EMBL/GenBank/DDBJ feature-table  
syntax.  See:

   http://bugzilla.open-bio.org/show_bug.cgi?id=1319

This is fixed in BioPerl 1.5.1, I believe, and maybe even in 1.4

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
         215-746-7018 (PCBI, 1428 Blockley Hall)
fax:    215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

Re: [GUSDEV] Extending the Schema to add a schema for pathway data

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

If you want to use GUS objects and write GusApplication plugins for 
these tables, then you need to convert the BioPax schema. If you want to 
just query the data (SQL or WDK) and assign your GUS entities to these 
pathways, you can get away without translating the schema to GUS 
conventions and adding materialized view relating them (or querying on 
the fly for the associations).  Your answer really depends on the needs 
of your application and your available coding resources.

In either case, I would replicate the BioPax database in a different 
schema, since translating from DB to DB is slightly easier in a plugin 
than flat file to DB transformations.

Angel

Dhivya Aras wrote:

> Hi,
>  
> I'm trying to add a new schema to GUS to add pathway data. I plan to 
> implement the biopax pathway data model on GUS. To do this, can I just 
> add the tables as they are given in Biopax? Or do I need to follow the 
> superclass(imp class)-subclass(view) relationship that is used in GUS?
>  
> I need to import data into the schema later on which is in BioPax 
> format, so I feel it would be easier to maintain the data model as 
> given in Biopax. But I just wanted to know if it would cause problems 
> since I'll be violating the subclassing relationships followed in GUS.
>  
> thanks
> dhivya
>
>
> ------------------------------------------------------------------------
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> PhotoMail 
> <http://us.rd.yahoo.com/mail_us/taglines/PMall/*http://photomail.mail.yahoo.com> 
> - it's free and works with Yahoo! Mail. 



-- 

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] About Extending the Schema

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

Comments inline...  read all the way to the bottom for my thoughts on 
the original issue.

Angel Pizarro wrote:
> 1) I'll update the wiki for to delete the old information.
> 
> 2) There is no mention of adding the new table definitions to the 
> gus_schema.xml file, which should be _the_ canonical version of the 
> schema from which perl, ddl and java code should be generated from. This 
> guide was probably written while the DBAdmin project was not stable.
> 

No, the guide was written after DBAdmin stabilized, but the thought was 
that end users (who the guide was written for) weren't likely to be 
modifying this file (more likely, they'd directly add their tables to 
the DB and want objects generated).  The XML file is quite large, with 
many references and dependencies, and was never really intended to be 
edited by hand, another reason there is no documentation for doing so (I 
never really did this either beyond simply precision changes).

> We have to make a decision as a community whether we want to continue 
> GUS as either a database driven or spec file driven documentation and 
> development. Currently it is both, depending on the task.

I disagree with this.  I maintain that as of 3.5, GUS is spec file 
driven.  Either way, that'd be my vote too.

(More below)

  Pretty
> confusing. My vote is for spec-file driven.
> 
> -angel
> 
> 
> Steve Fischer wrote:
> 
>> jian-
>>
>> gus_schema.xml is the right file to touch.
>>
>> we have definitely extended the schema here recently.  hopefully 
>> someone at cbil who has done so will answer this.  if not, please 
>> write back, and i'll look into it.
>>

I *think* you may have to add the new schema to the gus_config file. 
New objects don't need to be in XML, but they do need to be in the 
metadata tables (databaseinfo and tableinfo) and I think in the config 
file as well.  The system doesn't really support adding new schemas in a 
good way... you may also have to add the schemas to the build.xml file ( 
there's an open issue for resolving this).

--Mike

>> steve
>>
>> Jian Lu wrote:
>>
>>> I was using
>>> $touch $PROJECT_HOME/GUS/Schema/gus_schema.xml
>>>
>>> from 
>>> http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722 
>>>
>>>
>>> I could try what you mentioned here. Thanks.
>>>
>>> Angel Pizarro wrote:
>>>
>>>>
>>>> Did you "touch" the schema VERSION file prior to building? From the 
>>>> wiki:
>>>>
>>>> http://www.gusdb.org/wiki/index.php/Installing%20GUS
>>>>
>>>>
>>>>        Regenerating the GUS Perl and Java Objects
>>>>
>>>> touch $PROJECT_HOME/GUS/Model/schema/VERSION
>>>> build GUS install -append
>>>>
>>>>
>>>> Jian Lu wrote:
>>>>
>>>>> Hi GUS,
>>>>>
>>>>> I created a new schema name called APP with some new tables. I 
>>>>> registered APP to Core.DatabaseInfo and all new tables to 
>>>>> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the 
>>>>> new schema APP.
>>>>>
>>>>> When talking about extending GUS schema like adding new tables, 
>>>>> does it mean all new tables have to fall into existing GUS schema 
>>>>> such as DoTS? What should I do in order to support my own schema?
>>>>>
>>>>> Thanks.
>>>>>
>>>>> JL
>>>>>
>>>>>
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>>>>>
>>>>> _______________________________________________
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>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>
>>>
>>>
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> 
> 
> 
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[GUSDEV] Extending the Schema to add a schema for pathway data

[Dhivya A. <dhi...@ya...>]

Hi,
   
  I'm trying to add a new schema to GUS to add pathway data. I plan to implement the biopax pathway data model on GUS. To do this, can I just add the tables as they are given in Biopax? Or do I need to follow the superclass(imp class)-subclass(view) relationship that is used in GUS? 
   
  I need to import data into the schema later on which is in BioPax format, so I feel it would be easier to maintain the data model as given in Biopax. But I just wanted to know if it would cause problems since I'll be violating the subclassing relationships followed in GUS.
   
  thanks
  dhivya



		
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