gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] Sequence Type controlled vocab

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

folks-

Having looked at SO and MGED, I am not sure they are capturing what I 
have in mind, or, what we have captured in our SequenceType table

Here is the way I am thinking about breaking down "sequence type."   (If 
somebody can show me how these map into either of the ontologies Chris 
has mentioned that would be great).

For NA sequences:

Polymer Type
  - DNA
  - RNA
Molecule
  - chromosome
  - mRNA
  - tRNA
  - rRNA
  - oligo
Strandedness
  - single
  - double
Sequencing process
  - Genomic
  - EST
  - predicted
  - transcribed
  - what else?
Source
  - nucleus
  - mitochondria
  - plastid
  - plasmid
  - episome

Steve

Chris Stoeckert wrote:

> Steve,
> There are two complementary standards for sequence type. One comes 
> from the MGED Ontology.
> see 
> http://mged.sourceforge.net/ontologies/MGEDontology.php#BioSequenceType
> The other is SO  http://song.sourceforge.net/
> Chris
>
> On Feb 2, 2005, at 5:14 PM, Steve Fischer wrote:
>
>> folks-
>>
>> in gus we have a Dots.SequenceType table.
>>
>> here are the columns:
>> nucleotide_type
>> sub_type
>> strand
>> hierarchy    [should be hierarchy_depth]
>> parent_sequence_type_id
>> name
>> description
>>
>> First question:  does anybody know of an "emerging standard" for this?
>>
>> If there is one, then we should include it in the Controlled Vocabs 
>> that we package with GUS.
>>
>> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>>   - the one provided by Sanger on the wiki:  
>> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>>   - the one currently housed in CBIL's GUS instance
>>
>> As part of the GUS 3.5 install, we are getting serious about making 
>> the loading of CVs much easier.   A central part of that is making 
>> the CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>>
>> So, i am thinking that CBIL should chose one (or more) sequence type 
>> CVs to provide as downloads.  They could be offered in GUS XML format.
>>
>> Then, the automated GUS CV installer would find them from CBIL just 
>> like it will find GO from the GO Consortium.
>>
>> Any plugin that uses SequenceTypes should *not* hard code the 
>> transform, but, instead, take a SequenceTypeMapping file.  The file 
>> specifies the mapping from input sequence type to that stored in gus 
>> (by name).  The plugin should pre-scan the input file to detect if 
>> there are any illegal sequence types, and warn the user before 
>> loading any data
>>
>> If users find sequence types that the CBIL CV is missing, they can 
>> propose them via the mailing list.
>>
>> The objective is to:
>> 1. work with the fact that different input files for a plugin may use 
>> different sequence types
>> 2. get out of the business of ad hoc changes to the sequence types 
>> stored in the db
>>
>> comments?
>>
>> steve
>>
>> as a candidate CV the Sequence the SequenceTypesCV as developed by
>>
>> If not, then, how about this.   Plugins that depend on sequence type 
>> use a standard config file for sequence type.  (this might apply to 
>> other loose CVs).  The config file specifies the
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
>> Tool for open source databases. Create drag-&-drop reports. Save time
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>
>
>
>
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Re: [Gusdev-gusdev] Sequence Type controlled vocab

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

Steve,
There are two complementary standards for sequence type. One comes from 
the MGED Ontology.
see 
http://mged.sourceforge.net/ontologies/MGEDontology.php#BioSequenceType
The other is SO  http://song.sourceforge.net/
Chris

On Feb 2, 2005, at 5:14 PM, Steve Fischer wrote:

> folks-
>
> in gus we have a Dots.SequenceType table.
>
> here are the columns:
> nucleotide_type
> sub_type
> strand
> hierarchy    [should be hierarchy_depth]
> parent_sequence_type_id
> name
> description
>
> First question:  does anybody know of an "emerging standard" for this?
>
> If there is one, then we should include it in the Controlled Vocabs 
> that we package with GUS.
>
> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>   - the one provided by Sanger on the wiki:  
> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>   - the one currently housed in CBIL's GUS instance
>
> As part of the GUS 3.5 install, we are getting serious about making 
> the loading of CVs much easier.   A central part of that is making the 
> CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>
> So, i am thinking that CBIL should chose one (or more) sequence type 
> CVs to provide as downloads.  They could be offered in GUS XML format.
>
> Then, the automated GUS CV installer would find them from CBIL just 
> like it will find GO from the GO Consortium.
>
> Any plugin that uses SequenceTypes should *not* hard code the 
> transform, but, instead, take a SequenceTypeMapping file.  The file 
> specifies the mapping from input sequence type to that stored in gus 
> (by name).  The plugin should pre-scan the input file to detect if 
> there are any illegal sequence types, and warn the user before loading 
> any data
>
> If users find sequence types that the CBIL CV is missing, they can 
> propose them via the mailing list.
>
> The objective is to:
> 1. work with the fact that different input files for a plugin may use 
> different sequence types
> 2. get out of the business of ad hoc changes to the sequence types 
> stored in the db
>
> comments?
>
> steve
>
> as a candidate CV the Sequence the SequenceTypesCV as developed by
>
> If not, then, how about this.   Plugins that depend on sequence type 
> use a standard config file for sequence type.  (this might apply to 
> other loose CVs).  The config file specifies the
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
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Re: [Gusdev-gusdev] Sequence Type controlled vocab

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

mike raises the point that the CV we publish should not be in GUS XML 
format, but, in a system neutral format.

then we would need a dedicated plugin like LoadCBILSequenceTypes that 
would read that format.

steve

Steve Fischer wrote:

> folks-
>
> in gus we have a Dots.SequenceType table.
>
> here are the columns:
> nucleotide_type
> sub_type
> strand
> hierarchy    [should be hierarchy_depth]
> parent_sequence_type_id
> name
> description
>
> First question:  does anybody know of an "emerging standard" for this?
>
> If there is one, then we should include it in the Controlled Vocabs 
> that we package with GUS.
>
> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>   - the one provided by Sanger on the wiki:  
> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>   - the one currently housed in CBIL's GUS instance
>
> As part of the GUS 3.5 install, we are getting serious about making 
> the loading of CVs much easier.   A central part of that is making the 
> CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>
> So, i am thinking that CBIL should chose one (or more) sequence type 
> CVs to provide as downloads.  They could be offered in GUS XML format.
>
> Then, the automated GUS CV installer would find them from CBIL just 
> like it will find GO from the GO Consortium.
>
> Any plugin that uses SequenceTypes should *not* hard code the 
> transform, but, instead, take a SequenceTypeMapping file.  The file 
> specifies the mapping from input sequence type to that stored in gus 
> (by name).  The plugin should pre-scan the input file to detect if 
> there are any illegal sequence types, and warn the user before loading 
> any data
>
> If users find sequence types that the CBIL CV is missing, they can 
> propose them via the mailing list.
>
> The objective is to:
> 1. work with the fact that different input files for a plugin may use 
> different sequence types
> 2. get out of the business of ad hoc changes to the sequence types 
> stored in the db
>
> comments?
>
> steve
>
> as a candidate CV the Sequence the SequenceTypesCV as developed by
>
> If not, then, how about this.   Plugins that depend on sequence type 
> use a standard config file for sequence type.  (this might apply to 
> other loose CVs).  The config file specifies the
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] Sequence Type controlled vocab

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

folks-

in gus we have a Dots.SequenceType table.

here are the columns:
 nucleotide_type
 sub_type
 strand
 hierarchy    [should be hierarchy_depth]
 parent_sequence_type_id
 name
 description

First question:  does anybody know of an "emerging standard" for this?

If there is one, then we should include it in the Controlled Vocabs that 
we package with GUS.

Otherwise, we have, I think, two candidate SequenceTypeCVs:
   - the one provided by Sanger on the wiki:  
http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
   - the one currently housed in CBIL's GUS instance

As part of the GUS 3.5 install, we are getting serious about making the 
loading of CVs much easier.   A central part of that is making the CVs 
available from CBIL's download site (eg, the CBIL anatomy CV).

So, i am thinking that CBIL should chose one (or more) sequence type CVs 
to provide as downloads.  They could be offered in GUS XML format.

Then, the automated GUS CV installer would find them from CBIL just like 
it will find GO from the GO Consortium.

Any plugin that uses SequenceTypes should *not* hard code the transform, 
but, instead, take a SequenceTypeMapping file.  The file specifies the 
mapping from input sequence type to that stored in gus (by name).  The 
plugin should pre-scan the input file to detect if there are any illegal 
sequence types, and warn the user before loading any data

If users find sequence types that the CBIL CV is missing, they can 
propose them via the mailing list.

The objective is to:
 1. work with the fact that different input files for a plugin may use 
different sequence types
 2. get out of the business of ad hoc changes to the sequence types 
stored in the db

comments?

steve

as a candidate CV the Sequence the SequenceTypesCV as developed by

If not, then, how about this.   Plugins that depend on sequence type use 
a standard config file for sequence type.  (this might apply to other 
loose CVs).  The config file specifies the

[Gusdev-gusdev] Another necessary field

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

According to the schema browser, DoTS.NAFeature has
the field review_status_id which of course
points to a row in the table SRes.ReviewStatus.
However, in my installation of GUS, schema version 3.0,
DoTS.NAFeature lacks this field.

Such a thing would be very useful to have to distinguish
between the annotation of the same sequence by
different organizations.

In fact, I could use this field right now.  Does
schema version 3.2 have this field?  If so,
can someone suggest a patch/rebuild method
so that I could at least upgrade the NAFeature
table in my installation?

Thanks, 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

RE: [Gusdev-gusdev] Problem building WDK on Fedora

[Dave B. <db...@pc...>]

Hey Folks,

OK a few thoughts on the Postgres issue.

Here at CBIL, we don't have a good platform for testing the Postgres 
implementation of the WDK.  (Indeed, it is all we can do to handle 
Oracle!)  We are thrilled that other groups are working on it and 
encourage them to continue to do so, in the spirit of collaboration and 
getting results.

However, we think it is best if the extent of Postgres changes is 
limited to the file org.gusdb.wdk.model.implementation.PostgreSQL.java. 
The reason I mention this is that the BiowebDB team has sent out their fix 
for the Postgres bugs, but this fix has been applied to the ResultFactory 
class, as well as some of the wdk executables.  These other files are 
intended to be platform independent, and modifying them may affect other 
implementations of the WDK (ie Oracle).  If there is a place where 
ResultFactory must be changed to handle a specific implementation, then we 
should factor that part of the code into the database implementation 
classes rather than changing ResultFactory (and the wdk commands) 
themselves.

Therefore, we discourage changing ResultFactory class, and cannot provide 
support for any changes you might make, particularly as new releases of 
the WDK become available.  Instead, we would rather that groups who need 
to make these changes write to the wdkdev list with their requirements and 
we will be able to change the code together.  We will begin this process 
next week with the current issues with Postgres.

Sorry for the inconvenience.  We understand that we are a little biased 
towards Oracle here at CBIL and again appreciate collaborative efforts.

Dave

On Fri, 28 Jan 2005, Dave Barkan wrote:

> Hey Alberto,
>
> Here is what I have so far.  Sorry I don't have the complete solution but I 
> don't have any sort of setup yet on a Postgres instance, I will see what I 
> can do about getting that set up on our side for better debugging.
>
> First of all, your assertion here:
>
>> In the "PostgreSQL.java" file we edited:
>> 
>> line 117:
>> String alterSql = "alter table " + tableName + " add i varchar(100)";
>> 
>> We changed "number(12)" to "varchar(100)" because in the next line it makes 
>> an update and try to insert characters in that field that was "number(12)" 
>> then it was only accepting numbers.
>  >
>
> The next line you mention (line 123) is
>
> String rownumSql = "update " + tableName + " set i = " + tableName + 
> "_sq.nextval";
>
> Now that should evaluate to "update query_result_2 set i = 
> query_result_2_sq.nextval"
>
> and query_result_2_sq.nextval is the proper way to call the next value in the 
> primary key sequence for that table, right?  So that should evaluate to a 
> number, not a string.  I am not sure why it is evaluating to 
> "query_result_2_sq" as it seems to be in your code...where did the ".nextval" 
> go??
>
> Can you make sure that line 123 is what I think it should be above?  Sorry to 
> be obtuse about this, but just make sure you are using WDK version 1.1 or 
> later for this, I remember we made some PostGres upgrades at some point and 
> they were all incorporated into 1.1.  (as a side note, we have 1.2 out if you 
> want to work with that instead).
>
> Regardless, that column should remain a number, not the string it is above.
>
> Let us handle the ResultFactory issue after we solve this one because they 
> might be related.  I will continute to investigate.
>
> Dave
>> 
>> In "ResultFactory.java", lines 312 until 346:
>> 
>> In the following error, it assumes the "nextID" variable as being
>> "gus.QueryInstance_pkseq" and returns the error because this field should 
>> receive a numeric value: we changed the variable to a numeric value (in the 
>> script) to test and the data were inserted with success.
>> 
>> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
>> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
>> Failed executing sql:
>> insert into gus.QueryInstance (query_instance_id, query_name, cached,
>> session_id, dataset_name, start_time, param0, param1) values
>> (gus.QueryInstance_pkseq, 'RnaIds.ByDbESTLib', 1, null, null, now(),
>> '6', '80')
>> 
>> org.gusdb.wdk.model.WdkModelException:
>> org.postgresql.util.PSQLException: ERROR: relation "gus" does not
>> exist
>
>
>> 
>> 
>> -----------------------------------------------------------------------------------------------------------
>> After debugging that, we got this:
>> 
>> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
>> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
>> 92484435         query_result_2_sq
>> 92484471         query_result_2_sq
>> 92484523         query_result_2_sq
>> 92484578         query_result_2_sq
>> 92484601         query_result_2_sq
>> 92484678         query_result_2_sq
>> 92484682         query_result_2_sq
>> 92484686         query_result_2_sq
>> 92484695         query_result_2_sq
>> 92484703         query_result_2_sq
>> 92484708         query_result_2_sq
>> 92484710         query_result_2_sq
>> 92484731         query_result_2_sq
>> 92484741         query_result_2_sq
>> 92484752         query_result_2_sq
>> 92484755         query_result_2_sq
>> 92484758         query_result_2_sq
>> 92484764         query_result_2_sq
>> 92484767         query_result_2_sq
>> 92484768         query_result_2_sq
>> 92484772         query_result_2_sq
>> 92484779         query_result_2_sq
>> 92484780         query_result_2_sq
>> 92484801         query_result_2_sq
>> 92484835         query_result_2_sq
>> 92484836         query_result_2_sq
>> 101853404        query_result_2_sq
>> 
>> So... is the latter the expected output for "wdkQuery" ? If so, then looks 
>> like we have lot of debugging to do, if not maybe we are just not 
>> invoking/using the commands properly... as usual, any further suggestions 
>> are greatly appreciated ;-)
>> 
>> Alberto
>> 
>> 
>
>
> -------------------------------------------------------
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> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
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>

Re: [Gusdev-gusdev] Problem building WDK on Fedora

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

Folks-

We at Penn have not tested  the PostgresSQL stuff in the wdk, and are=20
not really set up to do so yet.    you brazilian guys should feel free=20
to play with PostgreSql.java to get things to work.

steve

Poliana Mateus wrote:

>O erro que o Dave menciona....j=E1 foi restaurado no arquivo. Realmente
>deveria receber um n=FAmero....enfim, ele voltou ao original.
>S=F3 alterei de "number(12)" para "numeric(12)".
>
>Abra=E7o,
>Poliana
>
>
>On Fri, 28 Jan 2005 14:01:53 -0500 (EST), Dave Barkan
><db...@pc...> wrote:
> =20
>
>>Hey Alberto,
>>
>>Here is what I have so far.  Sorry I don't have the complete solution b=
ut
>>I don't have any sort of setup yet on a Postgres instance, I will see w=
hat
>>I can do about getting that set up on our side for better debugging.
>>
>>First of all, your assertion here:
>>
>>   =20
>>
>>>In the "PostgreSQL.java" file we edited:
>>>
>>>line 117:
>>>String alterSql =3D "alter table " + tableName + " add i varchar(100)"=
;
>>>
>>>We changed "number(12)" to "varchar(100)" because in the next line it =
makes an update and try to insert characters in that field that was "numb=
er(12)" then it was only accepting numbers.
>>>     =20
>>>
>>   >
>>
>>The next line you mention (line 123) is
>>
>>String rownumSql =3D "update " + tableName + " set i =3D " + tableName =
+
>>"_sq.nextval";
>>
>>Now that should evaluate to "update query_result_2 set i =3D
>>query_result_2_sq.nextval"
>>
>>and query_result_2_sq.nextval is the proper way to call the next value
>>in the primary key sequence for that table, right?  So that should
>>evaluate to a number, not a string.  I am not sure why it is evaluating=
 to
>>"query_result_2_sq" as it seems to be in your code...where did the
>>".nextval" go??
>>
>>Can you make sure that line 123 is what I think it should be above?  So=
rry
>>to be obtuse about this, but just make sure you are using WDK version 1=
.1
>>or later for this, I remember we made some PostGres upgrades at some po=
int
>>and they were all incorporated into 1.1.  (as a side note, we have 1.2 =
out
>>if you want to work with that instead).
>>
>>Regardless, that column should remain a number, not the string it is
>>above.
>>
>>Let us handle the ResultFactory issue after we solve this one because t=
hey
>>might be related.  I will continute to investigate.
>>
>>Dave
>>   =20
>>
>>>In "ResultFactory.java", lines 312 until 346:
>>>
>>>In the following error, it assumes the "nextID" variable as being
>>>"gus.QueryInstance_pkseq" and returns the error because this field sho=
uld receive a numeric value: we changed the variable to a numeric value (=
in the script) to test and the data were inserted with success.
>>>
>>>[poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
>>>RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
>>>Failed executing sql:
>>>insert into gus.QueryInstance (query_instance_id, query_name, cached,
>>>session_id, dataset_name, start_time, param0, param1) values
>>>(gus.QueryInstance_pkseq, 'RnaIds.ByDbESTLib', 1, null, null, now(),
>>>'6', '80')
>>>
>>>org.gusdb.wdk.model.WdkModelException:
>>>org.postgresql.util.PSQLException: ERROR: relation "gus" does not
>>>exist
>>>     =20
>>>
>>>----------------------------------------------------------------------=
-------------------------------------
>>>After debugging that, we got this:
>>>
>>>[poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
>>>RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
>>>92484435         query_result_2_sq
>>>92484471         query_result_2_sq
>>>92484523         query_result_2_sq
>>>92484578         query_result_2_sq
>>>92484601         query_result_2_sq
>>>92484678         query_result_2_sq
>>>92484682         query_result_2_sq
>>>92484686         query_result_2_sq
>>>92484695         query_result_2_sq
>>>92484703         query_result_2_sq
>>>92484708         query_result_2_sq
>>>92484710         query_result_2_sq
>>>92484731         query_result_2_sq
>>>92484741         query_result_2_sq
>>>92484752         query_result_2_sq
>>>92484755         query_result_2_sq
>>>92484758         query_result_2_sq
>>>92484764         query_result_2_sq
>>>92484767         query_result_2_sq
>>>92484768         query_result_2_sq
>>>92484772         query_result_2_sq
>>>92484779         query_result_2_sq
>>>92484780         query_result_2_sq
>>>92484801         query_result_2_sq
>>>92484835         query_result_2_sq
>>>92484836         query_result_2_sq
>>>101853404        query_result_2_sq
>>>
>>>So... is the latter the expected output for "wdkQuery" ? If so, then l=
ooks like we have lot of debugging to do, if not maybe we are just not in=
voking/using the commands properly... as usual, any further suggestions a=
re greatly appreciated ;-)
>>>
>>>Alberto
>>>
>>>
>>>     =20
>>>

Re: [Gusdev-gusdev] Problem building WDK on Fedora

[Poliana M. <pol...@gm...>]

O erro que o Dave menciona....j=E1 foi restaurado no arquivo. Realmente
deveria receber um n=FAmero....enfim, ele voltou ao original.
S=F3 alterei de "number(12)" para "numeric(12)".

Abra=E7o,
Poliana


On Fri, 28 Jan 2005 14:01:53 -0500 (EST), Dave Barkan
<db...@pc...> wrote:
> Hey Alberto,
>=20
> Here is what I have so far.  Sorry I don't have the complete solution but
> I don't have any sort of setup yet on a Postgres instance, I will see wha=
t
> I can do about getting that set up on our side for better debugging.
>=20
> First of all, your assertion here:
>=20
> > In the "PostgreSQL.java" file we edited:
> >
> > line 117:
> > String alterSql =3D "alter table " + tableName + " add i varchar(100)";
> >
> > We changed "number(12)" to "varchar(100)" because in the next line it m=
akes an update and try to insert characters in that field that was "number(=
12)" then it was only accepting numbers.
>    >
>=20
> The next line you mention (line 123) is
>=20
> String rownumSql =3D "update " + tableName + " set i =3D " + tableName +
> "_sq.nextval";
>=20
> Now that should evaluate to "update query_result_2 set i =3D
> query_result_2_sq.nextval"
>=20
> and query_result_2_sq.nextval is the proper way to call the next value
> in the primary key sequence for that table, right?  So that should
> evaluate to a number, not a string.  I am not sure why it is evaluating t=
o
> "query_result_2_sq" as it seems to be in your code...where did the
> ".nextval" go??
>=20
> Can you make sure that line 123 is what I think it should be above?  Sorr=
y
> to be obtuse about this, but just make sure you are using WDK version 1.1
> or later for this, I remember we made some PostGres upgrades at some poin=
t
> and they were all incorporated into 1.1.  (as a side note, we have 1.2 ou=
t
> if you want to work with that instead).
>=20
> Regardless, that column should remain a number, not the string it is
> above.
>=20
> Let us handle the ResultFactory issue after we solve this one because the=
y
> might be related.  I will continute to investigate.
>=20
> Dave
> >
> > In "ResultFactory.java", lines 312 until 346:
> >
> > In the following error, it assumes the "nextID" variable as being
> > "gus.QueryInstance_pkseq" and returns the error because this field shou=
ld receive a numeric value: we changed the variable to a numeric value (in =
the script) to test and the data were inserted with success.
> >
> > [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> > RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> > Failed executing sql:
> > insert into gus.QueryInstance (query_instance_id, query_name, cached,
> > session_id, dataset_name, start_time, param0, param1) values
> > (gus.QueryInstance_pkseq, 'RnaIds.ByDbESTLib', 1, null, null, now(),
> > '6', '80')
> >
> > org.gusdb.wdk.model.WdkModelException:
> > org.postgresql.util.PSQLException: ERROR: relation "gus" does not
> > exist
>=20
> >
> > -----------------------------------------------------------------------=
------------------------------------
> > After debugging that, we got this:
> >
> > [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> > RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> > 92484435         query_result_2_sq
> > 92484471         query_result_2_sq
> > 92484523         query_result_2_sq
> > 92484578         query_result_2_sq
> > 92484601         query_result_2_sq
> > 92484678         query_result_2_sq
> > 92484682         query_result_2_sq
> > 92484686         query_result_2_sq
> > 92484695         query_result_2_sq
> > 92484703         query_result_2_sq
> > 92484708         query_result_2_sq
> > 92484710         query_result_2_sq
> > 92484731         query_result_2_sq
> > 92484741         query_result_2_sq
> > 92484752         query_result_2_sq
> > 92484755         query_result_2_sq
> > 92484758         query_result_2_sq
> > 92484764         query_result_2_sq
> > 92484767         query_result_2_sq
> > 92484768         query_result_2_sq
> > 92484772         query_result_2_sq
> > 92484779         query_result_2_sq
> > 92484780         query_result_2_sq
> > 92484801         query_result_2_sq
> > 92484835         query_result_2_sq
> > 92484836         query_result_2_sq
> > 101853404        query_result_2_sq
> >
> > So... is the latter the expected output for "wdkQuery" ? If so, then lo=
oks like we have lot of debugging to do, if not maybe we are just not invok=
ing/using the commands properly... as usual, any further suggestions are gr=
eatly appreciated ;-)
> >
> > Alberto
> >
> >
>

RE: [Gusdev-gusdev] Problem building WDK on Fedora

[Dave B. <db...@pc...>]

Hey Alberto,

Here is what I have so far.  Sorry I don't have the complete solution but 
I don't have any sort of setup yet on a Postgres instance, I will see what 
I can do about getting that set up on our side for better debugging.

First of all, your assertion here:

> In the "PostgreSQL.java" file we edited:
>
> line 117:
> String alterSql = "alter table " + tableName + " add i varchar(100)";
>
> We changed "number(12)" to "varchar(100)" because in the next line it makes an update and try to insert characters in that field that was "number(12)" then it was only accepting numbers.
   >

The next line you mention (line 123) is

String rownumSql = "update " + tableName + " set i = " + tableName + 
"_sq.nextval";

Now that should evaluate to "update query_result_2 set i = 
query_result_2_sq.nextval"

and query_result_2_sq.nextval is the proper way to call the next value 
in the primary key sequence for that table, right?  So that should 
evaluate to a number, not a string.  I am not sure why it is evaluating to 
"query_result_2_sq" as it seems to be in your code...where did the 
".nextval" go??

Can you make sure that line 123 is what I think it should be above?  Sorry 
to be obtuse about this, but just make sure you are using WDK version 1.1 
or later for this, I remember we made some PostGres upgrades at some point 
and they were all incorporated into 1.1.  (as a side note, we have 1.2 out 
if you want to work with that instead).

Regardless, that column should remain a number, not the string it is 
above.

Let us handle the ResultFactory issue after we solve this one because they 
might be related.  I will continute to investigate.

Dave
>
> In "ResultFactory.java", lines 312 until 346:
>
> In the following error, it assumes the "nextID" variable as being
> "gus.QueryInstance_pkseq" and returns the error because this field should receive a numeric value: we changed the variable to a numeric value (in the script) to test and the data were inserted with success.
>
> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> Failed executing sql:
> insert into gus.QueryInstance (query_instance_id, query_name, cached,
> session_id, dataset_name, start_time, param0, param1) values
> (gus.QueryInstance_pkseq, 'RnaIds.ByDbESTLib', 1, null, null, now(),
> '6', '80')
>
> org.gusdb.wdk.model.WdkModelException:
> org.postgresql.util.PSQLException: ERROR: relation "gus" does not
> exist


>
> -----------------------------------------------------------------------------------------------------------
> After debugging that, we got this:
>
> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> 92484435         query_result_2_sq
> 92484471         query_result_2_sq
> 92484523         query_result_2_sq
> 92484578         query_result_2_sq
> 92484601         query_result_2_sq
> 92484678         query_result_2_sq
> 92484682         query_result_2_sq
> 92484686         query_result_2_sq
> 92484695         query_result_2_sq
> 92484703         query_result_2_sq
> 92484708         query_result_2_sq
> 92484710         query_result_2_sq
> 92484731         query_result_2_sq
> 92484741         query_result_2_sq
> 92484752         query_result_2_sq
> 92484755         query_result_2_sq
> 92484758         query_result_2_sq
> 92484764         query_result_2_sq
> 92484767         query_result_2_sq
> 92484768         query_result_2_sq
> 92484772         query_result_2_sq
> 92484779         query_result_2_sq
> 92484780         query_result_2_sq
> 92484801         query_result_2_sq
> 92484835         query_result_2_sq
> 92484836         query_result_2_sq
> 101853404        query_result_2_sq
>
> So... is the latter the expected output for "wdkQuery" ? If so, then looks like we have lot of debugging to do, if not maybe we are just not invoking/using the commands properly... as usual, any further suggestions are greatly appreciated ;-)
>
> Alberto
>
>

[Gusdev-gusdev] GUS 3.5

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

I found out recently that the spam filter at Bellsouth
gradually but effectively took me off this list for the past
two months, so I apologize for any duplication.  I've got two
months worth of postings to parse this weekend.

However, I want to make sure that one thing does appear in the
3.5 release.

We've found that a number of subclass_views on NaFeatureImp do
NOT inheirit all of the named fields.  This may also be the
case with some of the views on NaSequenceImp and AAFeatureImp.
 I have already hacked the SQL that creates these to add them
for our crypto release.  We need sub_class views to inheirit
all named fields of the parent table.

One other thing I would also like to see is that we add some
of our controlled vocabularies to the release because plugins
sometimes MUST make assumptions about these vocabularies. 
However, this can wait for another release.

-Ed



-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

RE: [Gusdev-gusdev] Problem building WDK on Fedora

[Dave B. <db...@pc...>]

Hey Alberto,

Nice work on the debugging, but the final result of wdkQuery that you 
included is not the expected output.

From what I can tell, the problem arises in using the Postgres Sequence. 
In these tables, we are actually trying to insert the next primary key of 
a table as defined by the Sequence for that table.  Unfortunately, instead 
it looks like we are getting a string that is the name of the sequence! 
(query_result_2_sq, for example).  I will look into this; not sure exactly 
what the problem is yet.

Dave

On Wed, 26 Jan 2005, davila wrote:

> Hi Dave,
>
> Please have a look on what we have done...
>
> Errors description when running "wdkQuery":
>
> In the "PostgreSQL.java" file we edited:
>
> line 117:
> String alterSql = "alter table " + tableName + " add i varchar(100)";
>
> We changed "number(12)" to "varchar(100)" because in the next line it makes an update and try to insert characters in that field that was "number(12)" then it was only accepting numbers.
>
> Error:
> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> Failed executing sql:
> update query_result_2 set i = ('query_result_2_sq')
>
> org.gusdb.wdk.model.WdkModelException:
> org.postgresql.util.PSQLException: ERROR: invalid input syntax for
> type numeric: " query_result_2_sq"
>
> org.gusdb.wdk.model.WdkModelException:
> org.postgresql.util.PSQLException: ERROR: invalid input syntax for
> type numeric: " query_result_2_sq"
>
> ----------------------------------------------------------------------------------------------------------------------
>
> Yet in the "PostgreSQL.java" file we changed line 56:
>
>       return " select LOCALTIMESTAMP(0)"; to:
>
>        return "LOCALTIMESTAMP(0)";
>
> The "select" was removed then postgresql can recognize that.
>
> ----------------------------------------------------------------------------------------------------------------------
>
> In "ResultFactory.java", lines 312 until 346:
>
> In the following error, it assumes the "nextID" variable as being
> "gus.QueryInstance_pkseq" and returns the error because this field should receive a numeric value: we changed the variable to a numeric value (in the script) to test and the data were inserted with success.
>
> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> Failed executing sql:
> insert into gus.QueryInstance (query_instance_id, query_name, cached,
> session_id, dataset_name, start_time, param0, param1) values
> (gus.QueryInstance_pkseq, 'RnaIds.ByDbESTLib', 1, null, null, now(),
> '6', '80')
>
> org.gusdb.wdk.model.WdkModelException:
> org.postgresql.util.PSQLException: ERROR: relation "gus" does not
> exist
>
> org.gusdb.wdk.model.WdkModelException:
> org.postgresql.util.PSQLException: ERROR: relation "gus" does not
> exist
>
> -----------------------------------------------------------------------------------------------------------
> After debugging that, we got this:
>
> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> 92484435         query_result_2_sq
> 92484471         query_result_2_sq
> 92484523         query_result_2_sq
> 92484578         query_result_2_sq
> 92484601         query_result_2_sq
> 92484678         query_result_2_sq
> 92484682         query_result_2_sq
> 92484686         query_result_2_sq
> 92484695         query_result_2_sq
> 92484703         query_result_2_sq
> 92484708         query_result_2_sq
> 92484710         query_result_2_sq
> 92484731         query_result_2_sq
> 92484741         query_result_2_sq
> 92484752         query_result_2_sq
> 92484755         query_result_2_sq
> 92484758         query_result_2_sq
> 92484764         query_result_2_sq
> 92484767         query_result_2_sq
> 92484768         query_result_2_sq
> 92484772         query_result_2_sq
> 92484779         query_result_2_sq
> 92484780         query_result_2_sq
> 92484801         query_result_2_sq
> 92484835         query_result_2_sq
> 92484836         query_result_2_sq
> 101853404        query_result_2_sq
>
> So... is the latter the expected output for "wdkQuery" ? If so, then looks like we have lot of debugging to do, if not maybe we are just not invoking/using the commands properly... as usual, any further suggestions are greatly appreciated ;-)
>
> Alberto
>
>
> -----Original Message-----
> From:	Dave Barkan [mailto:db...@pc...]
> Sent:	Tue 1/25/2005 2:05 PM
> To:	davila
> Cc:	Steve Fischer; Michael Saffitz; marc jackson; gus...@li...; yo...@de...; pol...@gm...; Linair Maria Campos; Pablo Mendes
> Subject:	Re: [Gusdev-gusdev] Problem building WDK on Fedora
> The wdkXml command is working fine.  That means that the provided model
> has no errors in it (thank goodness).
>
> The problem with the following command
>
>> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
>> RnaIds.ByDbESTLib  -params NumEstLibs 6 ApiTaxon "Neospora caninum"
>
> is that ApiTaxon is no longer a paramter used in that query (as the
> message indicates).  You probably took that command from our wdk
> wiki documentation;  apparently the command is out of date and will be changed.  Sorry about
> that!  Try running the following command to test wdkQuery:
>
> % wdkQuery -model toyModel -query RnaIds.ByDbESTLib
>   -params NumEstLibs 6 AssemblyConsistency 80
>
>> Also, may we ask for any further example on how to use the WDK
>> utilities ?
>
> Examples to use the other wdk utilities are provided on the wdk wiki.  I
> checked them and they are up to date and should work.  If you need the
> url for that, here it is:
>
> http://www.gusdb.org/wiki/index.php/Gus%20Wdk%201.1
>
> Let me know if there is anything else.
>
> Thanks,
> Dave
>
>
>>
>> Thanks, Alberto
>>
>>
>>
>> On Thu, 2005-01-20 at 17:45 -0500, Dave Barkan wrote:
>>> Hey Alberto,
>>>
>>> Sorry for the delay on this; it is an issue with the Regression test which
>>> we supply with the WDK project.  You might be right that it is a problem
>>> with the path.  I will take a look.
>>>
>>> For now, failures in the regression test do not necessarily indicate a
>>> critical issue with your installation of the WDK, especially if the
>>> wdkSanity test works.  However, the regression test does need some
>>> tweaking to account for recent changes to expected behavior, so I will
>>> check it out and report back.
>>>
>>> Thanks,
>>> Dave
>>>
>>> On Tue, 18 Jan 2005, Alberto Davila wrote:
>>>
>>>> Thanks Steve !
>>>>
>>>> We managed to pass that error.
>>>>
>>>> Now, when trying "wdkRegressionTest":
>>>>
>>>> [poliana@phytomonas gus_home]$ wdkRegressionTest
>>>> --commandListFile=/usr/local/GUS/gus_home/data/WDKToySite/Model/regressionTest/sampleRegressionTestCommands
>>>>
>>>> running regression test newCacheTest
>>>>
>>>> sh: line 1: /newCacheTest.out: Permission denied
>>>> diff: /newCacheTest.out: No such file or directory
>>>> diff:
>>>> /usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/newCacheTest.out:
>>>> No such file or directory
>>>>
>>>> Error!  Test newCacheTest failed!
>>>> The observed result of the test was different than the expected result
>>>> of a test previously run.
>>>> To see the difference, run diff /newCacheTest.out
>>>> /usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/newCacheTest.out
>>>>
>>>> Received error in critical test newCacheTest.  Ending regression test
>>>> at /usr/local/GUS/gus_home/bin/wdkRegressionTest line 115, <GEN0> line
>>>> 3.
>>>>
>>>> Is the path
>>>> "/usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/newCacheTest.out"
>>>> correct ? Just realized we have this PATH:
>>>> "/usr/local/GUS/gus_home/data/WDKToySite/Model/regressionTest" instead.
>>>>
>>>> Regards, Alberto
>>>>
>>>>
>>>>
>>>> At 20:44 17/1/2005, Steve Fischer wrote:
>>>>> i think the problem is that we have the oracle driver hard coded.
>>>>>
>>>>> take a look in $PROJECT_HOME/WDK/Model/bin/wdkCache.
>>>>>
>>>>> my $cmd = "java -Djdbc.drivers=oracle.jdbc.driver.OracleDriver
>>>>> -DconfigDir=$GUS_HOME/config -DcmdName=wdkCache -classpath $CLASSPATH
>>>>> org.gusdb.wdk.model.ResultFactory $args";
>>>>>
>>>>> as a workaround, in the files in that directory, change to postgres
>>>>> drivers.
>>>>>
>>>>> we'll make it configurable.
>>>>>
>>>>> you'll also need to write a new class for postrgres.
>>>>>
>>>>> the Oracle version is:
>>>>>
>>>>> $PROJECT_HOME/WDK/Model/src/java/org/gusdb/wdk/model/implementation/Oracle.java
>>>>>
>>>>> you'll need to make a similar class for postgres.   then, in the file
>>>>> $PROJECT_HOME/WDKToySite/Model/config/toyModel-config.xml
>>>>>
>>>>> you'll need to refer to that class:
>>>>> <modelConfig login="yourLoginHere"
>>>>>         password="yourPasswordHere"
>>>>>         connectionUrl="yourConnectionUrlHere"
>>>>>         queryInstanceTable="QueryInstance"
>>>>>         maxQueryParams="50"
>>>>>         platformClass="org.gusdb.wdk.model.implementation.Oracle"
>>>>>             initialSize="3"
>>>>>             maxActive="20"
>>>>>             maxIdle="3"
>>>>>             minIdle="3"
>>>>>             maxWait="500"/>
>>>>>
>>>>>
>>>>>
>>>>> Alberto Davila wrote:
>>>>>
>>>>>> Hi Dave,
>>>>>>
>>>>>> You are right... that output seem to be fine... however we cannot use WDK,
>>>>>> here are more logs:
>>>>>>
>>>>>> [poliana@phytomonas gus_home]$ wdkCache -model toyModel -new
>>>>>>
>>>>>> Making cache table gus.QueryInstance
>>>>>>
>>>>>> Failed executing sql:
>>>>>> create table gus.QueryInstance (query_instance_id number(12) not null,
>>>>>> query_name varchar2(100) not null, cached number(1) not
>>>>>> null,result_table varchar2(30), start_time date not null, end_time
>>>>>> date, dataset_name varchar2(100), session_id varchar2(50), param0
>>>>>> varchar2(200), param1 varchar2(200), param2 varchar2(200), param3
>>>>>> varchar2(200), param4 varchar2(200), param5 varchar2(200), param6
>>>>>> varchar2(200), param7 varchar2(200), param8 varchar2(200), param9
>>>>>> varchar2(200), param10 varchar2(200), param11 varchar2(200), param12
>>>>>> varchar2(200), param13 varchar2(200), param14 varchar2(200), param15
>>>>>> varchar2(200), param16 varchar2(200), param17 varchar2(200), param18
>>>>>> varchar2(200), param19 varchar2(200), param20 varchar2(200), param21
>>>>>> varchar2(200), param22 varchar2(200), param23 varchar2(200), param24
>>>>>> varchar2(200), param25 varchar2(200), param26 varchar2(200), param27
>>>>>> varchar2(200), param28 varchar2(200), param29 varchar2(200), param30
>>>>>> varchar2(200), param31 varchar2(200), param32 varchar2(200), param33
>>>>>> varchar2(200), param34 varchar2(200), param35 varchar2(200), param36
>>>>>> varchar2(200), param37 varchar2(200), param38 varchar2(200), param39
>>>>>> varchar2(200), param40 varchar2(200), param41 varchar2(200), param42
>>>>>> varchar2(200), param43 varchar2(200), param44 varchar2(200), param45
>>>>>> varchar2(200), param46 varchar2(200), param47 varchar2(200), param48
>>>>>> varchar2(200), param50 varchar2(200))
>>>>>>
>>>>>> FAILED
>>>>>>
>>>>>> org.gusdb.wdk.model.WdkModelException: java.sql.SQLException: No suitable
>>>>>> driver
>>>>>>         at
>>>>>> org.gusdb.wdk.model.ResultFactory.createCache(ResultFactory.java:136)
>>>>>>         at org.gusdb.wdk.model.ResultFactory.main(ResultFactory.java:524)
>>>>>> Caused by: java.sql.SQLException: No suitable driver
>>>>>>         at java.sql.DriverManager.getConnection(DriverManager.java:532)
>>>>>>         at java.sql.DriverManager.getConnection(DriverManager.java:171)
>>>>>>         at
>>>>>> org.apache.commons.dbcp.DriverManagerConnectionFactory.createConnection(DriverManagerConnectionFactory.java:94)
>>>>>>         at
>>>>>> org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:300)
>>>>>>         at
>>>>>> org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:816)
>>>>>>         at
>>>>>> org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:140)
>>>>>>         at
>>>>>> org.gusdb.wdk.model.implementation.SqlUtils.execute(SqlUtils.java:206)
>>>>>>         at
>>>>>> org.gusdb.wdk.model.ResultFactory.createCache(ResultFactory.java:127)
>>>>>>         ... 1 more
>>>>>>
>>>>>>
>>>>>> We have the Postgres JDBC installed and its PATH (export
>>>>>> CLASSPATH=/usr/local/GUS/gus_home/lib/java/pg74.215.jdbc3.jar) properly
>>>>>> set (such as stated in the manual, we have choosen the JDBC version based
>>>>>> on jsdk and postgres installed versions), then decided to make a test with
>>>>>> the JDBC (just in case...) :
>>>>>>
>>>>>> [poliana@phytomonas gus_home]$ java -classpath . HelloPostgresql banco
>>>>>> user 'senha'
>>>>>> hello
>>>>>>
>>>>>> Connection to PostgreSQL 7.4.6 successful.
>>>>>>
>>>>>> Executing this command: create table jdbc_demo (code int, text
>>>>>> varchar(20))
>>>>>>
>>>>>> Executing this command: insert into jdbc_demo values (1,'One')
>>>>>>
>>>>>> Executing this command twice: insert into jdbc_demo values (3,'Four')
>>>>>>
>>>>>> Executing this command: update jdbc_demo set text = 'Three' where code = 3
>>>>>>
>>>>>> 2 rows were update by this statement
>>>>>>
>>>>>>
>>>>>>
>>>>>> Now demostrating a prepared statement...
>>>>>> The Statement looks like this: insert into jdbc_demo values (?,?)
>>>>>>
>>>>>> Looping three times filling in the fields...
>>>>>>
>>>>>> 10...
>>>>>>
>>>>>> 11...
>>>>>>
>>>>>> 12...
>>>>>>
>>>>>> Now executing the command: select * from jdbc_demo
>>>>>> code = 1; text = One
>>>>>>
>>>>>> code = 3; text = Three
>>>>>>
>>>>>> code = 3; text = Three
>>>>>>
>>>>>> code = 10; text = HiHo
>>>>>>
>>>>>> code = 11; text = HiHo
>>>>>>
>>>>>> code = 12; text = HiHo
>>>>>>
>>>>>> Executing this command: drop table jdbc_demo
>>>>>>
>>>>>> Could it be that the command "wdkCache -model toyModel -new" is trying to
>>>>>> build the WDK based on the "Oracle version of GUS" ? We are using the
>>>>>> Postgres version built with the scripts from Jeetendra...
>>>>>>
>>>>>> Thanks in advance for any further help ;-)
>>>>>>
>>>>>> Cheers, Alberto
>>>>>>
>>>>>>
>>>>>>
>>>>>> At 12:50 13/1/2005, Dave Barkan wrote:
>>>>>>
>>>>>>> Hi Alberto,
>>>>>>>
>>>>>>> The output that you sent is actually fine!  There are no error messages
>>>>>>> that I can see, and the output indicates that you built successfully.
>>>>>>> The "no existing files, doing nothing" message is a simple statement that
>>>>>>> shouldn't concern you.
>>>>>>>
>>>>>>> Are there any other symptoms that lead you to believe there is a problem
>>>>>>> with the build?
>>>>>>>
>>>>>>> Dave
>>>>>>>
>>>>>>> On Thu, 13 Jan 2005, Alberto Davila wrote:
>>>>>>>
>>>>>>>> HI Dave,
>>>>>>>>
>>>>>>>> Thanks...
>>>>>>>>
>>>>>>>> I think we made a mistake trying to build "GUS" instead the
>>>>>>>> "WDKToySite", then we started again, have a look:
>>>>>>>>
>>>>>>>> [poliana@phytomonas gus_home]$ build WDKToySite install -append
>>>>>>>>
>>>>>>>> ant -f /usr/local/GUS/project_home/install/build.xml install
>>>>>>>> -Dproj=WDKToySite -DtargetDir=/usr/local/GUS/gus_home -Dcomp=
>>>>>>>> -DprojectsDir=/usr/local/GUS/project_home   -Dappend=true   -logger
>>>>>>>> org.apache.tools.ant.NoBannerLogger  | grep ']'
>>>>>>>>
>>>>>>>>     [echo] .
>>>>>>>>     [echo] Installing WDK/Model
>>>>>>>>     [copy] Copying 13 files to /usr/local/GUS/gus_home/bin
>>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/xml
>>>>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/xml
>>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/rng
>>>>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/rng
>>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/perl/WDK/Model
>>>>>>>>     [copy] Copying 24 files to
>>>>>>>> /usr/local/GUS/gus_home/lib/perl/WDK/Model
>>>>>>>>     [copy] Copying 10 files to /usr/local/GUS/gus_home/lib/java
>>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/doc/WDK/Model
>>>>>>>>     [copy] Copying 9 files to /usr/local/GUS/gus_home/doc/WDK/Model
>>>>>>>>      [jar] Building jar: /usr/local/GUS/gus_home/lib/java/WDK-Model.jar
>>>>>>>>     [echo] .
>>>>>>>>     [echo] IMPORTANT REMINDER: If you have not already done so,
>>>>>>>> please copy any .jar needed for database connectivity (such as
>>>>>>>> oracle-classes12.jar) into /usr/local/GUS/gus_home/lib/java.  The WDK
>>>>>>>> does not supply these.  See the installation instructions available at
>>>>>>>> www.gusdb.org/wdk for details.
>>>>>>>>     [echo] .
>>>>>>>>     [echo] .
>>>>>>>>     [echo] Installing WDK/Controller
>>>>>>>>     [copy] Copying 3 files to /usr/local/GUS/gus_home/lib/java
>>>>>>>>      [jar] Building jar:
>>>>>>>> /usr/local/GUS/gus_home/lib/java/WDK-Controller.jar
>>>>>>>>     [echo] .
>>>>>>>>     [echo] Installing WDK/View
>>>>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/java
>>>>>>>>   [concat] No existing files and no nested text, doing nothing
>>>>>>>>     [echo] .
>>>>>>>>     [echo] Installing WDKToySite/Model
>>>>>>>>     [copy] Copying 5 files to /usr/local/GUS/gus_home/config
>>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/doc/WDKToySite/Model
>>>>>>>>     [copy] Copying 1 file to
>>>>>>>> /usr/local/GUS/gus_home/doc/WDKToySite/Model
>>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/data/WDKToySite/Model
>>>>>>>>     [copy] Copying 13 files to
>>>>>>>> /usr/local/GUS/gus_home/data/WDKToySite/Model
>>>>>>>>   [concat] No existing files and no nested text, doing nothing
>>>>>>>>
>>>>>>>> Here is our ".bashrc" file:
>>>>>>>>
>>>>>>>> [root@phytomonas poliana]# more .bashrc
>>>>>>>> # .bashrc
>>>>>>>>
>>>>>>>> PATH=$PATH:/usr/local/pgsql/bin; export PATH
>>>>>>>> PATH=$PATH:/usr/java/j2sdk1.4.2_06/bin; export PATH
>>>>>>>> PATH=$PATH:/usr/local/apache-ant-1.6.2/bin; export PATH
>>>>>>>> export ANT_HOME=/usr/local/apache-ant-1.6.2
>>>>>>>> export JAVA_HOME=/usr/java/j2sdk1.4.2_06
>>>>>>>> export CATALINA_HOME=/usr/local/jakarta-tomcat-5.0.28
>>>>>>>> export GUS_HOME=/usr/local/GUS/gus_home
>>>>>>>> export PROJECT_HOME=/usr/local/GUS/project_home
>>>>>>>> export GUS_CONFIG_FILE=$GUS_HOME/.gus.properties
>>>>>>>> PATH=$GUS_HOME/bin:$PROJECT_HOME/install/bin:$ANT_HOME/bin:$PATH; export
>>>>>>>> PATH
>>>>>>>> export PERL5LIB=/usr/local/GUS/gus_home/lib/perl
>>>>>>>>
>>>>>>>> Here is the software/system we are using:
>>>>>>>>
>>>>>>>> Ant: apache-ant-1.6.2
>>>>>>>> TomCat: jakarta-tomcat-5.0.28
>>>>>>>> Java: Java(TM) 2 Runtime Environment, Standard Edition (build
>>>>>>>> 1.4.2_06-b03)
>>>>>>>> Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
>>>>>>>> Postgres: postgresql-7.4.6
>>>>>>>> Perl: 5.8.3
>>>>>>>> Fedora Core 1
>>>>>>>> Kernel: 2.4.22-1.2199.nptl
>>>>>>>>
>>>>>>>> and, we are using the scripts for the "PostgreSQL" version posted by
>>>>>>>> Jeetendra (by the way, Jeetendra plugins are working fine, "SubmitRow"
>>>>>>>> went OK then just using "LoadTaxon", the load iof the latter is taking
>>>>>>>> more than 48 hours ... and still running...)
>>>>>>>>
>>>>>>>> any further suggestions to debug the WDK install ?
>>>>>>>>
>>>>>>>> Thanks, Alberto
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> At 13:49 10/1/2005, Dave Barkan wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>> This error message is usually indicative of the build system being
>>>>>>>>> unable to connect to your database instance.
>>>>>>>>> Make sure that you have configured your $GUS_CONFIG_FILE and your
>>>>>>>>> environment variables as detailed in steps 5 and 9 of the GUS
>>>>>>>>> installation instructions at
>>>>>>>>> http://www.gusdb.org/documentation/install-setup.html
>>>>>>>>> Off the top of my head, that is the most likely solution to your
>>>>>>>>> problem, but if that doesn't work, I would suggest asking your DBA if
>>>>>>>>> they can think of anything regarding your local connection and database
>>>>>>>>> instance.
>>>>>>>>> Dave
>>>>>>>>> On Fri, 7 Jan 2005, davila wrote:
>>>>>>>>>
>>>>>>>>>> Hi Marc,
>>>>>>>>>> We just tried to install the WDK 1.1. by using:
>>>>>>>>>> build GUS install -append
>>>>>>>>>> then got this errors:
>>>>>>>>>> ...
>>>>>>>>>>    [javac]
>>>>>>>>>> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFamilyExperiment_Table.java:24:
>>>>>>>>>> illegal start of expression
>>>>>>>>>>    [javac]         tableAtts.put("modification_date", new
>>>>>>>>>> GUSTableAttribute("modification_date", "date", "java.lang.notdefyet",
>>>>>>>>>> -1, , -1, false, false) );
>>>>>>>>>>    [javac]             ^
>>>>>>>>>>    [javac]
>>>>>>>>>> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFamilyExperiment_Table.java:24:
>>>>>>>>>> ')' expected
>>>>>>>>>>    [javac]         tableAtts.put("modification_date", new
>>>>>>>>>> GUSTableAttribute("modification_date", "date", "java.lang.notdefyet",
>>>>>>>>>> -1, , -1, false, false) );
>>>>>>>>>>    [javac]                                  ^
>>>>>>>>>>    [javac] 100 errors
>>>>>>>>>> BUILD FAILED
>>>>>>>>>> /usr/local/GUS/project_home/install/build.xml:26: The following error
>>>>>>>>>> occurred while executing this line:
>>>>>>>>>> /usr/local/GUS/project_home/GUS/build.xml:73: The following error
>>>>>>>>>> occurred while executing this line:
>>>>>>>>>> /usr/local/GUS/project_home/install/build.xml:221: The following error
>>>>>>>>>> occurred while executing this line:
>>>>>>>>>> /usr/local/GUS/project_home/install/build.xml:240: Compile failed; see
>>>>>>>>>> the compiler error output for details.
>>>>>>>>>> I saw you got a similar problem and solved it. Could you kindly share
>>>>>>>>>> how did you solve that ?
>>>>>>>>>> We use:
>>>>>>>>>> Java: Java(TM) 2 Runtime Environment, Standard Edition (build
>>>>>>>>>> 1.4.2_06-b03)
>>>>>>>>>> Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
>>>>>>>>>> Apache Ant version 1.6.2 compiled on July 16 2004
>>>>>>>>>> Thanks, Alberto
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> From: marc jackson <dechon@ho...>
>>>>>>>>>> Re: problems building gus on redhat linux
>>>>>>>>>> 2004-12-17 10:21
>>>>>>>>>> That wasn"t it, but things are resolved.  For now. :)
>>>>>>>>>> Thanks for your help!
>>>>>>>>>> Regards,
>>>>>>>>>> Marc
>>>>>>>>>> &gt;From: Steve Fischer &lt;sfischer@pc...&gt;
>>>>>>>>>> &gt;To: marc jackson &lt;dechon@ho...&gt;
>>>>>>>>>> &gt;CC: gusdev-gusdev@li...
>>>>>>>>>> &gt;Subject: Re: [Gusdev-gusdev] problems building gus on redhat linux
>>>>>>>>>> &gt;Date: Fri, 17 Dec 2004 07:36:37 -0500
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;Marc-
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;i suspect that you haven"t defined the environment variable
>>>>>>>>>> &gt;$GUS_CONFIG_FILE.
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;it should be discussed in the docs.
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;steve
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;[sfischer@cottus ~]$ echo $GUS_CONFIG_FILE
>>>>>>>>>> &gt;/home/sfischer/.gus.properties
>>>>>>>>>> &gt;[sfischer@cottus ~]$ more $GUS_CONFIG_FILE
>>>>>>>>>> &gt;databaseLogin=your_login
>>>>>>>>>> &gt;databasePassword=your_password
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;readOnlyDatabaseLogin=your_login
>>>>>>>>>> &gt;readOnlyDatabasePassword=your_password
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;dbiDsn=dbi:Oracle:host=cbilbld.pcbi.upenn.edu;sid=cbilbld
>>>>>>>>>> #your
>>>>>>>>>> &gt;dsn string here
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;coreSchemaName=Core
>>>>>>>>>> &gt;userName=sfischer     #your user name here
>>>>>>>>>> &gt;group=CBIL     # your group name here
>>>>>>>>>> &gt;project=GUS   # your project here
>>>>>>>>>> &gt;[sfischer@cottus ~]$
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;marc jackson wrote:
>>>>>>>>>> &gt;
>>>>>>>>>> &gt;&gt;Hello,
>>>>>>>>>> &gt;&gt;  I"m having a problem getting GUS to install/compile. I"ve
>>>>>>>>>> been
>>>>>>>>>> &gt;&gt;able to configure the database, but when I go to run the
>>>>>>>>>> &quot;ga&quot;
>>>>>>>>>> &gt;&gt;command to bootstrap in data. it pukes.  In working with Ed
>>>>>>>>>> &gt;&gt;Robinson, we got to the 2nd build.  Specifically:
>>>>>>>>>> &gt;&gt;  build GUS install -append returns the following error:
>>>>>>>>>> &gt;&gt;    [exec] Required property "group" must be specified in  at
>>>>>>>>>> &gt;&gt;/opt/gus/gus_home/lib/perl/CBIL/Util/PropertySet.pm line 53.
>>>>>>>>>> &gt;&gt;BUILD FAILED
>>>>>>>>>> &gt;&gt;/opt/gus/project_home/install/build.xml:26: The following
>>>>>>>>>> error
>>>>>>>>>> &gt;&gt;occurred while executing this line:
>>>>>>>>>> &gt;&gt;/opt/gus/project_home/GUS/build.xml:190: exec returned: -1
>>>>>>>>>> &gt;&gt;  any help would be appreacited.
>>>>>>>>>> &gt;&gt;  Regards,
>>>>>>>>>> &gt;&gt;  Marc
>>>>
>>>>
>

Re: [Gusdev-gusdev] GUS 3.5 Release

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

On Jan 26, 2005, at 3:22 PM, davila wrote:

> Could you share any further info/details on your CDAT initiative ?... 
> sure, tables should support (help to differentiate) gene trees from 
> species trees, (phylogenomics ?) etc.

I'll attempt to summarize CDAT (Character Data and Trees) for the group:

The basic premise of the CDAT schema is that you have a database of 
sequences (duh) and features on these sequences (using a very simple 
feature & feature_location schema, with the possibility of 
subfeatures), from which certain subsets (colloquially named 
"Families") may be involved in one (or more) multiple sequence 
alignments; in this case, each multiple sequence alignment is 
considered the result of a computational "experiment" (i.e. you might 
generate many different MSAs with a variety of approaches), and thus 
you may have many MSAs for a given Family (and a given sequence may 
participate in multiple Families).  Phylogenetic trees are then another 
layer of "experimental data" obtained from an MSA, which may generate 
many trees per MSA (think bootstrapping, in addition to alternative 
topology-estimation techniques).

CDAT spends much of it's "schema space" dealing with various 
phylogenetic aspects of the multiple sequence alignment itself 
(represented as a state matrix, with either individual sequence 
characters or in fact any character/feature "state" in a given cell of 
the matrix, where columns of the matrix represent positions in the MSA, 
and rows of the matrix represent separate OTUs).  Interestingly, this 
arrangement allows ancestral sequence/character/feature states (in a 
probabilistic framework) to also be stored and queried.

CDAT does not deal with species trees as an experimental datatype; 
rather, the NCBI taxonomy tree is assumed to be fixed.  However, this 
could easily be extended using the same logic as above.

In short, this schema flavor allows one to perform (what I think are) 
very interesting analyses, including (but of course not limited to):

* site-specific analysis of positive/negative selection in the context 
of sequence features (domains, PROSITE motifs, introns, secondary 
structure predictions, etc etc).
* ancestral feature state estimation (e.g. intron gain/loss events)
* measuring relationships between disparate sequence features (e.g. 
introns, domains, active sites, transcriptional binding sites, etc), 
with the possibility of filtering these relative to various 
evolutionary properties (orthology/paralogy, mutational rates, 
taxonomic slices, etc)

I must admit, there is a significant drawback to this schema: while 
powerful, the extreme normalization of character states yields 
thousands of rows for a given MSA (e.g. an MSA composed of 20 OTUs of 
500 character states yields 10,000 rows of state cells; any ancestral 
reconstruction will generate another 10,000 rows of data).  For 
10,000's of Families, this limits the utility of the database to only a 
very few (i.e. 1) experimental setups (but, conversely, for just a few 
1000 families, allows many alternative experiments to be considered).  
So I tend to have separate instantiations for each experimental study I 
perform.

-Aaron

--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  am...@pc...
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

Re: [Gusdev-gusdev] Inconsistency among Sequence tables

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

Yes, this is something we can easily fix and certainly should.
Chris
ps. I think this may reflect the history and bias of CBIL's view of 
GUS. The history is that when we started varchars were limited to 255 
but being NA-centric we fixed NASequence but not AASequence.

On Jan 26, 2005, at 4:07 PM, ju...@cs... wrote:

>
> As I continue to work with the ExternalAASequence view,
> I find another discrepancy with other Sequence views/tables.
>
> Compare the size the description field between NASequenceImp and
> AASequenceImp.
>
>  DoTS.NASequenceImp DESCRIPTION   VARCHAR2(2000)
>  DoTS.AASequenceImp DESCRIPTION   VARCHAR2(255)
>
> 255 characters is often two small to include the entire name
> of a sequence from a fasta file.  Enlarging the
> DoTS.AASequenceImp description field to 2000 and
> and passing this field to the several views on AASequenceImp
> would be greatly appreciated as well.
>
> Thanks, Josef
>
>
> Chris Stoeckert <sto...@pc...> writes:
>>
>> Hi Josef,
>> Your comments are very timely in light of our plans to release GUS 3.5
>> shortly which is meant to address issues such as you raise. Mike sent
>> mail earlier today on this but please see
>> http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>>
>> I think that you are right about the need for taxon_id. Note that it
>> should probably go in AASequenceImp (the table) and be inherited by 
>> all
>> views. Anyone have a problem with that for GUS 3.5?
>>
>> Note that both AASequence and ExternalAASequence are views with
>> AASequence as the "superclass" view. external_database_release_id is a
>> named attribute of the parent table and so is inherited by all views.
>>
>> Cheers,
>> Chris
>>
>> On Jan 25, 2005, at 3:15 PM, ju...@cs... wrote:
>>>
>>> I recently began working with the DoTS.ExternalAASequence table for
>>> the first time, and I noticed several discrepancies with this
>>> table and the DoTS.ExternalNASequence and DoTS.NASequence tables,
>>> one of which I feel is serious.
>>>
>>>                    name            taxon_id    description
>>> external_database_release_id
>>>                    varchar2(255)   number(12)  varchar2(2000)
>>> number(10)
>>>
>>> ExternalNASequence  yes            yes         yes              yes
>>> NASequence          no             yes         yes              no
>>> ExternalAASequence  yes            no          yes              yes
>>> AASequence          no             no          yes              yes
>>>
>>>
>>> Looking at the above chart, we see that both AASequence
>>> and ExternalAASequence lack the taxon_id.  This surely must
>>> be an oversight, I cannot imagine why such a thing
>>> could be intentional.
>>>
>>> A minor annoyance is that NASequence and AASequence lack a
>>> "name varchar2(255)" column and therefore must have all text
>>> regarding a sequence in the description column.  For query
>>> and display purposes, it is very useful to be
>>> able to refer to a sequence by a shorter handle.
>>>
>>>
> [...]
>
> Daphne Preuss Laboratory
> Molecular Genetics and Cell Biology
> The University of Chicago
> ju...@cs...
>
> voice: (773) 834-3985
> fax:   (773) 702-6648
>
>

Re: [Gusdev-gusdev] Inconsistency among Sequence tables

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

As I continue to work with the ExternalAASequence view,
I find another discrepancy with other Sequence views/tables.

Compare the size the description field between NASequenceImp and
AASequenceImp.

 DoTS.NASequenceImp DESCRIPTION   VARCHAR2(2000)
 DoTS.AASequenceImp DESCRIPTION   VARCHAR2(255)

255 characters is often two small to include the entire name
of a sequence from a fasta file.  Enlarging the
DoTS.AASequenceImp description field to 2000 and
and passing this field to the several views on AASequenceImp
would be greatly appreciated as well.

Thanks, Josef


Chris Stoeckert <sto...@pc...> writes:
>
> Hi Josef,
> Your comments are very timely in light of our plans to release GUS 3.5
> shortly which is meant to address issues such as you raise. Mike sent
> mail earlier today on this but please see
> http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>
> I think that you are right about the need for taxon_id. Note that it
> should probably go in AASequenceImp (the table) and be inherited by all
> views. Anyone have a problem with that for GUS 3.5?
>
> Note that both AASequence and ExternalAASequence are views with
> AASequence as the "superclass" view. external_database_release_id is a
> named attribute of the parent table and so is inherited by all views.
>
> Cheers,
> Chris
>
> On Jan 25, 2005, at 3:15 PM, ju...@cs... wrote:
> >
> > I recently began working with the DoTS.ExternalAASequence table for
> > the first time, and I noticed several discrepancies with this
> > table and the DoTS.ExternalNASequence and DoTS.NASequence tables,
> > one of which I feel is serious.
> >
> >                    name            taxon_id    description
> > external_database_release_id
> >                    varchar2(255)   number(12)  varchar2(2000)
> > number(10)
> >
> > ExternalNASequence  yes            yes         yes              yes
> > NASequence          no             yes         yes              no
> > ExternalAASequence  yes            no          yes              yes
> > AASequence          no             no          yes              yes
> >
> >
> > Looking at the above chart, we see that both AASequence
> > and ExternalAASequence lack the taxon_id.  This surely must
> > be an oversight, I cannot imagine why such a thing
> > could be intentional.
> >
> > A minor annoyance is that NASequence and AASequence lack a
> > "name varchar2(255)" column and therefore must have all text
> > regarding a sequence in the description column.  For query
> > and display purposes, it is very useful to be
> > able to refer to a sequence by a shorter handle.
> >
> >
[...]

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

voice: (773) 834-3985
fax:   (773) 702-6648

RE: [Gusdev-gusdev] GUS 3.5 Release

[davila <da...@io...>]

Hi Aaron, Mike,

Indeed, comparative genomics will receive major benefit from =
phylogeny/evolutionary analyses...=20

Could you share any further info/details on your CDAT initiative ?... =
sure, tables should support (help to differentiate) gene trees from =
species trees, (phylogenomics ?) etc.

I hope to be able to provide a draft schema for this next week or so, =
hope it is not too late...=20

Cheers, Alberto



-----Original Message-----
From:	Aaron J. Mackey [mailto:am...@pc...]
Sent:	Wed 1/26/2005 2:22 PM
To:	gusdev-gusdev
Cc:=09
Subject:	Re: [Gusdev-gusdev] GUS 3.5 Release

On Jan 26, 2005, at 11:13 AM, Michael Saffitz wrote:

> GUS doesn't currently support phylogeny/evolutionary data, but are=20
> very open to adding it to GUS.  Do you have a schema (rough or=20
> otherwise) in mind?

I think the upcoming comparative genomics efforts here (and elsewhere)=20
will certainly require support for evolutionary analyses.  I would=20
encourage those doing the schema design to consider both multiple=20
sequence alignments and trees (including associated bootstraps,=20
likelihood, branch lengths, etc) as experimental results that may be=20
computed in many different fashions.  I.e. don't fall into the trap of=20
the "one true tree", because it doesn't exist.

I'd be very interested to be involved in this effort, and to give a=20
talk on my own phylogenetic sequence database (CDAT) for consideration=20
as one possible schema to mimic.

-Aaron

--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  am...@pc...
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

RE: [Gusdev-gusdev] Problem building WDK on Fedora

[davila <da...@io...>]

Hi Dave,

Please have a look on what we have done...

Errors description when running "wdkQuery":

In the "PostgreSQL.java" file we edited:

line 117:
String alterSql =3D "alter table " + tableName + " add i varchar(100)";

We changed "number(12)" to "varchar(100)" because in the next line it =
makes an update and try to insert characters in that field that was =
"number(12)" then it was only accepting numbers.

Error:
[poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
Failed executing sql:
update query_result_2 set i =3D ('query_result_2_sq')
=20
org.gusdb.wdk.model.WdkModelException:
org.postgresql.util.PSQLException: ERROR: invalid input syntax for
type numeric: " query_result_2_sq"
=20
org.gusdb.wdk.model.WdkModelException:
org.postgresql.util.PSQLException: ERROR: invalid input syntax for
type numeric: " query_result_2_sq"

-------------------------------------------------------------------------=
---------------------------------------------

Yet in the "PostgreSQL.java" file we changed line 56:
       =20
       return " select LOCALTIMESTAMP(0)"; to:

        return "LOCALTIMESTAMP(0)";

The "select" was removed then postgresql can recognize that.

-------------------------------------------------------------------------=
---------------------------------------------

In "ResultFactory.java", lines 312 until 346:

In the following error, it assumes the "nextID" variable as being
"gus.QueryInstance_pkseq" and returns the error because this field =
should receive a numeric value: we changed the variable to a numeric =
value (in the script) to test and the data were inserted with success.

[poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
Failed executing sql:
insert into gus.QueryInstance (query_instance_id, query_name, cached,
session_id, dataset_name, start_time, param0, param1) values
(gus.QueryInstance_pkseq, 'RnaIds.ByDbESTLib', 1, null, null, now(),
'6', '80')
=20
org.gusdb.wdk.model.WdkModelException:
org.postgresql.util.PSQLException: ERROR: relation "gus" does not
exist
=20
org.gusdb.wdk.model.WdkModelException:
org.postgresql.util.PSQLException: ERROR: relation "gus" does not
exist

-------------------------------------------------------------------------=
----------------------------------
After debugging that, we got this:

[poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
92484435         query_result_2_sq
92484471         query_result_2_sq
92484523         query_result_2_sq
92484578         query_result_2_sq
92484601         query_result_2_sq
92484678         query_result_2_sq
92484682         query_result_2_sq
92484686         query_result_2_sq
92484695         query_result_2_sq
92484703         query_result_2_sq
92484708         query_result_2_sq
92484710         query_result_2_sq
92484731         query_result_2_sq
92484741         query_result_2_sq
92484752         query_result_2_sq
92484755         query_result_2_sq
92484758         query_result_2_sq
92484764         query_result_2_sq
92484767         query_result_2_sq
92484768         query_result_2_sq
92484772         query_result_2_sq
92484779         query_result_2_sq
92484780         query_result_2_sq
92484801         query_result_2_sq
92484835         query_result_2_sq
92484836         query_result_2_sq
101853404        query_result_2_sq

So... is the latter the expected output for "wdkQuery" ? If so, then =
looks like we have lot of debugging to do, if not maybe we are just not =
invoking/using the commands properly... as usual, any further =
suggestions are greatly appreciated ;-)

Alberto


-----Original Message-----
From:	Dave Barkan [mailto:db...@pc...]
Sent:	Tue 1/25/2005 2:05 PM
To:	davila
Cc:	Steve Fischer; Michael Saffitz; marc jackson; =
gus...@li...; yo...@de...; =
pol...@gm...; Linair Maria Campos; Pablo Mendes
Subject:	Re: [Gusdev-gusdev] Problem building WDK on Fedora
The wdkXml command is working fine.  That means that the provided model=20
has no errors in it (thank goodness).

The problem with the following command

> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib  -params NumEstLibs 6 ApiTaxon "Neospora caninum"

is that ApiTaxon is no longer a paramter used in that query (as the=20
message indicates).  You probably took that command from our wdk=20
wiki documentation;  apparently the command is out of date and will be =
changed.  Sorry about=20
that!  Try running the following command to test wdkQuery:

% wdkQuery -model toyModel -query RnaIds.ByDbESTLib
   -params NumEstLibs 6 AssemblyConsistency 80

> Also, may we ask for any further example on how to use the WDK
> utilities ?

Examples to use the other wdk utilities are provided on the wdk wiki.  I =

checked them and they are up to date and should work.  If you need the=20
url for that, here it is:

http://www.gusdb.org/wiki/index.php/Gus%20Wdk%201.1

Let me know if there is anything else.

Thanks,
Dave


>
> Thanks, Alberto
>
>
>
> On Thu, 2005-01-20 at 17:45 -0500, Dave Barkan wrote:
>> Hey Alberto,
>>
>> Sorry for the delay on this; it is an issue with the Regression test =
which
>> we supply with the WDK project.  You might be right that it is a =
problem
>> with the path.  I will take a look.
>>
>> For now, failures in the regression test do not necessarily indicate =
a
>> critical issue with your installation of the WDK, especially if the
>> wdkSanity test works.  However, the regression test does need some
>> tweaking to account for recent changes to expected behavior, so I =
will
>> check it out and report back.
>>
>> Thanks,
>> Dave
>>
>> On Tue, 18 Jan 2005, Alberto Davila wrote:
>>
>>> Thanks Steve !
>>>
>>> We managed to pass that error.
>>>
>>> Now, when trying "wdkRegressionTest":
>>>
>>> [poliana@phytomonas gus_home]$ wdkRegressionTest
>>> =
--commandListFile=3D/usr/local/GUS/gus_home/data/WDKToySite/Model/regress=
ionTest/sampleRegressionTestCommands
>>>
>>> running regression test newCacheTest
>>>
>>> sh: line 1: /newCacheTest.out: Permission denied
>>> diff: /newCacheTest.out: No such file or directory
>>> diff:
>>> =
/usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/n=
ewCacheTest.out:
>>> No such file or directory
>>>
>>> Error!  Test newCacheTest failed!
>>> The observed result of the test was different than the expected =
result
>>> of a test previously run.
>>> To see the difference, run diff /newCacheTest.out
>>> =
/usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/n=
ewCacheTest.out
>>>
>>> Received error in critical test newCacheTest.  Ending regression =
test
>>> at /usr/local/GUS/gus_home/bin/wdkRegressionTest line 115, <GEN0> =
line
>>> 3.
>>>
>>> Is the path
>>> =
"/usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/=
newCacheTest.out"
>>> correct ? Just realized we have this PATH:
>>> "/usr/local/GUS/gus_home/data/WDKToySite/Model/regressionTest" =
instead.
>>>
>>> Regards, Alberto
>>>
>>>
>>>
>>> At 20:44 17/1/2005, Steve Fischer wrote:
>>>> i think the problem is that we have the oracle driver hard coded.
>>>>
>>>> take a look in $PROJECT_HOME/WDK/Model/bin/wdkCache.
>>>>
>>>> my $cmd =3D "java -Djdbc.drivers=3Doracle.jdbc.driver.OracleDriver
>>>> -DconfigDir=3D$GUS_HOME/config -DcmdName=3DwdkCache -classpath =
$CLASSPATH
>>>> org.gusdb.wdk.model.ResultFactory $args";
>>>>
>>>> as a workaround, in the files in that directory, change to postgres
>>>> drivers.
>>>>
>>>> we'll make it configurable.
>>>>
>>>> you'll also need to write a new class for postrgres.
>>>>
>>>> the Oracle version is:
>>>>
>>>> =
$PROJECT_HOME/WDK/Model/src/java/org/gusdb/wdk/model/implementation/Oracl=
e.java
>>>>
>>>> you'll need to make a similar class for postgres.   then, in the =
file
>>>> $PROJECT_HOME/WDKToySite/Model/config/toyModel-config.xml
>>>>
>>>> you'll need to refer to that class:
>>>> <modelConfig login=3D"yourLoginHere"
>>>>         password=3D"yourPasswordHere"
>>>>         connectionUrl=3D"yourConnectionUrlHere"
>>>>         queryInstanceTable=3D"QueryInstance"
>>>>         maxQueryParams=3D"50"
>>>>         platformClass=3D"org.gusdb.wdk.model.implementation.Oracle"
>>>>             initialSize=3D"3"
>>>>             maxActive=3D"20"
>>>>             maxIdle=3D"3"
>>>>             minIdle=3D"3"
>>>>             maxWait=3D"500"/>
>>>>
>>>>
>>>>
>>>> Alberto Davila wrote:
>>>>
>>>>> Hi Dave,
>>>>>
>>>>> You are right... that output seem to be fine... however we cannot =
use WDK,
>>>>> here are more logs:
>>>>>
>>>>> [poliana@phytomonas gus_home]$ wdkCache -model toyModel -new
>>>>>
>>>>> Making cache table gus.QueryInstance
>>>>>
>>>>> Failed executing sql:
>>>>> create table gus.QueryInstance (query_instance_id number(12) not =
null,
>>>>> query_name varchar2(100) not null, cached number(1) not
>>>>> null,result_table varchar2(30), start_time date not null, end_time
>>>>> date, dataset_name varchar2(100), session_id varchar2(50), param0
>>>>> varchar2(200), param1 varchar2(200), param2 varchar2(200), param3
>>>>> varchar2(200), param4 varchar2(200), param5 varchar2(200), param6
>>>>> varchar2(200), param7 varchar2(200), param8 varchar2(200), param9
>>>>> varchar2(200), param10 varchar2(200), param11 varchar2(200), =
param12
>>>>> varchar2(200), param13 varchar2(200), param14 varchar2(200), =
param15
>>>>> varchar2(200), param16 varchar2(200), param17 varchar2(200), =
param18
>>>>> varchar2(200), param19 varchar2(200), param20 varchar2(200), =
param21
>>>>> varchar2(200), param22 varchar2(200), param23 varchar2(200), =
param24
>>>>> varchar2(200), param25 varchar2(200), param26 varchar2(200), =
param27
>>>>> varchar2(200), param28 varchar2(200), param29 varchar2(200), =
param30
>>>>> varchar2(200), param31 varchar2(200), param32 varchar2(200), =
param33
>>>>> varchar2(200), param34 varchar2(200), param35 varchar2(200), =
param36
>>>>> varchar2(200), param37 varchar2(200), param38 varchar2(200), =
param39
>>>>> varchar2(200), param40 varchar2(200), param41 varchar2(200), =
param42
>>>>> varchar2(200), param43 varchar2(200), param44 varchar2(200), =
param45
>>>>> varchar2(200), param46 varchar2(200), param47 varchar2(200), =
param48
>>>>> varchar2(200), param50 varchar2(200))
>>>>>
>>>>> FAILED
>>>>>
>>>>> org.gusdb.wdk.model.WdkModelException: java.sql.SQLException: No =
suitable
>>>>> driver
>>>>>         at
>>>>> =
org.gusdb.wdk.model.ResultFactory.createCache(ResultFactory.java:136)
>>>>>         at =
org.gusdb.wdk.model.ResultFactory.main(ResultFactory.java:524)
>>>>> Caused by: java.sql.SQLException: No suitable driver
>>>>>         at =
java.sql.DriverManager.getConnection(DriverManager.java:532)
>>>>>         at =
java.sql.DriverManager.getConnection(DriverManager.java:171)
>>>>>         at
>>>>> =
org.apache.commons.dbcp.DriverManagerConnectionFactory.createConnection(D=
riverManagerConnectionFactory.java:94)
>>>>>         at
>>>>> =
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConn=
ectionFactory.java:300)
>>>>>         at
>>>>> =
org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObject=
Pool.java:816)
>>>>>         at
>>>>> =
org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource=
.java:140)
>>>>>         at
>>>>> =
org.gusdb.wdk.model.implementation.SqlUtils.execute(SqlUtils.java:206)
>>>>>         at
>>>>> =
org.gusdb.wdk.model.ResultFactory.createCache(ResultFactory.java:127)
>>>>>         ... 1 more
>>>>>
>>>>>
>>>>> We have the Postgres JDBC installed and its PATH (export
>>>>> CLASSPATH=3D/usr/local/GUS/gus_home/lib/java/pg74.215.jdbc3.jar) =
properly
>>>>> set (such as stated in the manual, we have choosen the JDBC =
version based
>>>>> on jsdk and postgres installed versions), then decided to make a =
test with
>>>>> the JDBC (just in case...) :
>>>>>
>>>>> [poliana@phytomonas gus_home]$ java -classpath . HelloPostgresql =
banco
>>>>> user 'senha'
>>>>> hello
>>>>>
>>>>> Connection to PostgreSQL 7.4.6 successful.
>>>>>
>>>>> Executing this command: create table jdbc_demo (code int, text
>>>>> varchar(20))
>>>>>
>>>>> Executing this command: insert into jdbc_demo values (1,'One')
>>>>>
>>>>> Executing this command twice: insert into jdbc_demo values =
(3,'Four')
>>>>>
>>>>> Executing this command: update jdbc_demo set text =3D 'Three' =
where code =3D 3
>>>>>
>>>>> 2 rows were update by this statement
>>>>>
>>>>>
>>>>>
>>>>> Now demostrating a prepared statement...
>>>>> The Statement looks like this: insert into jdbc_demo values (?,?)
>>>>>
>>>>> Looping three times filling in the fields...
>>>>>
>>>>> 10...
>>>>>
>>>>> 11...
>>>>>
>>>>> 12...
>>>>>
>>>>> Now executing the command: select * from jdbc_demo
>>>>> code =3D 1; text =3D One
>>>>>
>>>>> code =3D 3; text =3D Three
>>>>>
>>>>> code =3D 3; text =3D Three
>>>>>
>>>>> code =3D 10; text =3D HiHo
>>>>>
>>>>> code =3D 11; text =3D HiHo
>>>>>
>>>>> code =3D 12; text =3D HiHo
>>>>>
>>>>> Executing this command: drop table jdbc_demo
>>>>>
>>>>> Could it be that the command "wdkCache -model toyModel -new" is =
trying to
>>>>> build the WDK based on the "Oracle version of GUS" ? We are using =
the
>>>>> Postgres version built with the scripts from Jeetendra...
>>>>>
>>>>> Thanks in advance for any further help ;-)
>>>>>
>>>>> Cheers, Alberto
>>>>>
>>>>>
>>>>>
>>>>> At 12:50 13/1/2005, Dave Barkan wrote:
>>>>>
>>>>>> Hi Alberto,
>>>>>>
>>>>>> The output that you sent is actually fine!  There are no error =
messages
>>>>>> that I can see, and the output indicates that you built =
successfully.
>>>>>> The "no existing files, doing nothing" message is a simple =
statement that
>>>>>> shouldn't concern you.
>>>>>>
>>>>>> Are there any other symptoms that lead you to believe there is a =
problem
>>>>>> with the build?
>>>>>>
>>>>>> Dave
>>>>>>
>>>>>> On Thu, 13 Jan 2005, Alberto Davila wrote:
>>>>>>
>>>>>>> HI Dave,
>>>>>>>
>>>>>>> Thanks...
>>>>>>>
>>>>>>> I think we made a mistake trying to build "GUS" instead the
>>>>>>> "WDKToySite", then we started again, have a look:
>>>>>>>
>>>>>>> [poliana@phytomonas gus_home]$ build WDKToySite install -append
>>>>>>>
>>>>>>> ant -f /usr/local/GUS/project_home/install/build.xml install
>>>>>>> -Dproj=3DWDKToySite -DtargetDir=3D/usr/local/GUS/gus_home =
-Dcomp=3D
>>>>>>> -DprojectsDir=3D/usr/local/GUS/project_home   -Dappend=3Dtrue   =
-logger
>>>>>>> org.apache.tools.ant.NoBannerLogger  | grep ']'
>>>>>>>
>>>>>>>     [echo] .
>>>>>>>     [echo] Installing WDK/Model
>>>>>>>     [copy] Copying 13 files to /usr/local/GUS/gus_home/bin
>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/xml
>>>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/xml
>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/rng
>>>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/rng
>>>>>>>    [mkdir] Created dir: =
/usr/local/GUS/gus_home/lib/perl/WDK/Model
>>>>>>>     [copy] Copying 24 files to
>>>>>>> /usr/local/GUS/gus_home/lib/perl/WDK/Model
>>>>>>>     [copy] Copying 10 files to /usr/local/GUS/gus_home/lib/java
>>>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/doc/WDK/Model
>>>>>>>     [copy] Copying 9 files to =
/usr/local/GUS/gus_home/doc/WDK/Model
>>>>>>>      [jar] Building jar: =
/usr/local/GUS/gus_home/lib/java/WDK-Model.jar
>>>>>>>     [echo] .
>>>>>>>     [echo] IMPORTANT REMINDER: If you have not already done so,
>>>>>>> please copy any .jar needed for database connectivity (such as
>>>>>>> oracle-classes12.jar) into /usr/local/GUS/gus_home/lib/java.  =
The WDK
>>>>>>> does not supply these.  See the installation instructions =
available at
>>>>>>> www.gusdb.org/wdk for details.
>>>>>>>     [echo] .
>>>>>>>     [echo] .
>>>>>>>     [echo] Installing WDK/Controller
>>>>>>>     [copy] Copying 3 files to /usr/local/GUS/gus_home/lib/java
>>>>>>>      [jar] Building jar:
>>>>>>> /usr/local/GUS/gus_home/lib/java/WDK-Controller.jar
>>>>>>>     [echo] .
>>>>>>>     [echo] Installing WDK/View
>>>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/java
>>>>>>>   [concat] No existing files and no nested text, doing nothing
>>>>>>>     [echo] .
>>>>>>>     [echo] Installing WDKToySite/Model
>>>>>>>     [copy] Copying 5 files to /usr/local/GUS/gus_home/config
>>>>>>>    [mkdir] Created dir: =
/usr/local/GUS/gus_home/doc/WDKToySite/Model
>>>>>>>     [copy] Copying 1 file to
>>>>>>> /usr/local/GUS/gus_home/doc/WDKToySite/Model
>>>>>>>    [mkdir] Created dir: =
/usr/local/GUS/gus_home/data/WDKToySite/Model
>>>>>>>     [copy] Copying 13 files to
>>>>>>> /usr/local/GUS/gus_home/data/WDKToySite/Model
>>>>>>>   [concat] No existing files and no nested text, doing nothing
>>>>>>>
>>>>>>> Here is our ".bashrc" file:
>>>>>>>
>>>>>>> [root@phytomonas poliana]# more .bashrc
>>>>>>> # .bashrc
>>>>>>>
>>>>>>> PATH=3D$PATH:/usr/local/pgsql/bin; export PATH
>>>>>>> PATH=3D$PATH:/usr/java/j2sdk1.4.2_06/bin; export PATH
>>>>>>> PATH=3D$PATH:/usr/local/apache-ant-1.6.2/bin; export PATH
>>>>>>> export ANT_HOME=3D/usr/local/apache-ant-1.6.2
>>>>>>> export JAVA_HOME=3D/usr/java/j2sdk1.4.2_06
>>>>>>> export CATALINA_HOME=3D/usr/local/jakarta-tomcat-5.0.28
>>>>>>> export GUS_HOME=3D/usr/local/GUS/gus_home
>>>>>>> export PROJECT_HOME=3D/usr/local/GUS/project_home
>>>>>>> export GUS_CONFIG_FILE=3D$GUS_HOME/.gus.properties
>>>>>>> =
PATH=3D$GUS_HOME/bin:$PROJECT_HOME/install/bin:$ANT_HOME/bin:$PATH; =
export
>>>>>>> PATH
>>>>>>> export PERL5LIB=3D/usr/local/GUS/gus_home/lib/perl
>>>>>>>
>>>>>>> Here is the software/system we are using:
>>>>>>>
>>>>>>> Ant: apache-ant-1.6.2
>>>>>>> TomCat: jakarta-tomcat-5.0.28
>>>>>>> Java: Java(TM) 2 Runtime Environment, Standard Edition (build
>>>>>>> 1.4.2_06-b03)
>>>>>>> Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
>>>>>>> Postgres: postgresql-7.4.6
>>>>>>> Perl: 5.8.3
>>>>>>> Fedora Core 1
>>>>>>> Kernel: 2.4.22-1.2199.nptl
>>>>>>>
>>>>>>> and, we are using the scripts for the "PostgreSQL" version =
posted by
>>>>>>> Jeetendra (by the way, Jeetendra plugins are working fine, =
"SubmitRow"
>>>>>>> went OK then just using "LoadTaxon", the load iof the latter is =
taking
>>>>>>> more than 48 hours ... and still running...)
>>>>>>>
>>>>>>> any further suggestions to debug the WDK install ?
>>>>>>>
>>>>>>> Thanks, Alberto
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> At 13:49 10/1/2005, Dave Barkan wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>> This error message is usually indicative of the build system =
being
>>>>>>>> unable to connect to your database instance.
>>>>>>>> Make sure that you have configured your $GUS_CONFIG_FILE and =
your
>>>>>>>> environment variables as detailed in steps 5 and 9 of the GUS
>>>>>>>> installation instructions at
>>>>>>>> http://www.gusdb.org/documentation/install-setup.html
>>>>>>>> Off the top of my head, that is the most likely solution to =
your
>>>>>>>> problem, but if that doesn't work, I would suggest asking your =
DBA if
>>>>>>>> they can think of anything regarding your local connection and =
database
>>>>>>>> instance.
>>>>>>>> Dave
>>>>>>>> On Fri, 7 Jan 2005, davila wrote:
>>>>>>>>
>>>>>>>>> Hi Marc,
>>>>>>>>> We just tried to install the WDK 1.1. by using:
>>>>>>>>> build GUS install -append
>>>>>>>>> then got this errors:
>>>>>>>>> ...
>>>>>>>>>    [javac]
>>>>>>>>> =
/usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFam=
ilyExperiment_Table.java:24:
>>>>>>>>> illegal start of expression
>>>>>>>>>    [javac]         tableAtts.put("modification_date", new
>>>>>>>>> GUSTableAttribute("modification_date", "date", =
"java.lang.notdefyet",
>>>>>>>>> -1, , -1, false, false) );
>>>>>>>>>    [javac]             ^
>>>>>>>>>    [javac]
>>>>>>>>> =
/usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFam=
ilyExperiment_Table.java:24:
>>>>>>>>> ')' expected
>>>>>>>>>    [javac]         tableAtts.put("modification_date", new
>>>>>>>>> GUSTableAttribute("modification_date", "date", =
"java.lang.notdefyet",
>>>>>>>>> -1, , -1, false, false) );
>>>>>>>>>    [javac]                                  ^
>>>>>>>>>    [javac] 100 errors
>>>>>>>>> BUILD FAILED
>>>>>>>>> /usr/local/GUS/project_home/install/build.xml:26: The =
following error
>>>>>>>>> occurred while executing this line:
>>>>>>>>> /usr/local/GUS/project_home/GUS/build.xml:73: The following =
error
>>>>>>>>> occurred while executing this line:
>>>>>>>>> /usr/local/GUS/project_home/install/build.xml:221: The =
following error
>>>>>>>>> occurred while executing this line:
>>>>>>>>> /usr/local/GUS/project_home/install/build.xml:240: Compile =
failed; see
>>>>>>>>> the compiler error output for details.
>>>>>>>>> I saw you got a similar problem and solved it. Could you =
kindly share
>>>>>>>>> how did you solve that ?
>>>>>>>>> We use:
>>>>>>>>> Java: Java(TM) 2 Runtime Environment, Standard Edition (build
>>>>>>>>> 1.4.2_06-b03)
>>>>>>>>> Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
>>>>>>>>> Apache Ant version 1.6.2 compiled on July 16 2004
>>>>>>>>> Thanks, Alberto
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> From: marc jackson <dechon@ho...>
>>>>>>>>> Re: problems building gus on redhat linux
>>>>>>>>> 2004-12-17 10:21
>>>>>>>>> That wasn"t it, but things are resolved.  For now. :)
>>>>>>>>> Thanks for your help!
>>>>>>>>> Regards,
>>>>>>>>> Marc
>>>>>>>>> &gt;From: Steve Fischer &lt;sfischer@pc...&gt;
>>>>>>>>> &gt;To: marc jackson &lt;dechon@ho...&gt;
>>>>>>>>> &gt;CC: gusdev-gusdev@li...
>>>>>>>>> &gt;Subject: Re: [Gusdev-gusdev] problems building gus on =
redhat linux
>>>>>>>>> &gt;Date: Fri, 17 Dec 2004 07:36:37 -0500
>>>>>>>>> &gt;
>>>>>>>>> &gt;Marc-
>>>>>>>>> &gt;
>>>>>>>>> &gt;i suspect that you haven"t defined the environment =
variable
>>>>>>>>> &gt;$GUS_CONFIG_FILE.
>>>>>>>>> &gt;
>>>>>>>>> &gt;it should be discussed in the docs.
>>>>>>>>> &gt;
>>>>>>>>> &gt;steve
>>>>>>>>> &gt;
>>>>>>>>> &gt;[sfischer@cottus ~]$ echo $GUS_CONFIG_FILE
>>>>>>>>> &gt;/home/sfischer/.gus.properties
>>>>>>>>> &gt;[sfischer@cottus ~]$ more $GUS_CONFIG_FILE
>>>>>>>>> &gt;databaseLogin=3Dyour_login
>>>>>>>>> &gt;databasePassword=3Dyour_password
>>>>>>>>> &gt;
>>>>>>>>> &gt;readOnlyDatabaseLogin=3Dyour_login
>>>>>>>>> &gt;readOnlyDatabasePassword=3Dyour_password
>>>>>>>>> &gt;
>>>>>>>>> =
&gt;dbiDsn=3Ddbi:Oracle:host=3Dcbilbld.pcbi.upenn.edu;sid=3Dcbilbld
>>>>>>>>> #your
>>>>>>>>> &gt;dsn string here
>>>>>>>>> &gt;
>>>>>>>>> &gt;coreSchemaName=3DCore
>>>>>>>>> &gt;userName=3Dsfischer     #your user name here
>>>>>>>>> &gt;group=3DCBIL     # your group name here
>>>>>>>>> &gt;project=3DGUS   # your project here
>>>>>>>>> &gt;[sfischer@cottus ~]$
>>>>>>>>> &gt;
>>>>>>>>> &gt;
>>>>>>>>> &gt;
>>>>>>>>> &gt;marc jackson wrote:
>>>>>>>>> &gt;
>>>>>>>>> &gt;&gt;Hello,
>>>>>>>>> &gt;&gt;  I"m having a problem getting GUS to install/compile. =
I"ve
>>>>>>>>> been
>>>>>>>>> &gt;&gt;able to configure the database, but when I go to run =
the
>>>>>>>>> &quot;ga&quot;
>>>>>>>>> &gt;&gt;command to bootstrap in data. it pukes.  In working =
with Ed
>>>>>>>>> &gt;&gt;Robinson, we got to the 2nd build.  Specifically:
>>>>>>>>> &gt;&gt;  build GUS install -append returns the following =
error:
>>>>>>>>> &gt;&gt;    [exec] Required property "group" must be specified =
in  at
>>>>>>>>> &gt;&gt;/opt/gus/gus_home/lib/perl/CBIL/Util/PropertySet.pm =
line 53.
>>>>>>>>> &gt;&gt;BUILD FAILED
>>>>>>>>> &gt;&gt;/opt/gus/project_home/install/build.xml:26: The =
following
>>>>>>>>> error
>>>>>>>>> &gt;&gt;occurred while executing this line:
>>>>>>>>> &gt;&gt;/opt/gus/project_home/GUS/build.xml:190: exec =
returned: -1
>>>>>>>>> &gt;&gt;  any help would be appreacited.
>>>>>>>>> &gt;&gt;  Regards,
>>>>>>>>> &gt;&gt;  Marc
>>>
>>>

Re: [Gusdev-gusdev] Inconsistency among Sequence tables

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

your request for a description field seems reasonable.  i'll look into 
it for 3.5

steve

Josef Jurek wrote:

>Chris Stoeckert <sto...@pc...> writes:
>  
>
>>Hi Josef,
>>Your comments are very timely in light of our plans to release GUS 3.5
>>shortly which is meant to address issues such as you raise. Mike sent
>>mail earlier today on this but please see
>>http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>>    
>>
>
>Great;
>
>Here is another inconsistency, which I have brought up
>on the list before. Both GeneFeature and NAFeature
>have a "name varchar2(30)" field though it
>is useful to store the entire text that a GenBank file
>may have for a feature.  GeneFeature has "gene varchar2(2000)"
>but NAFeature lacks a varchar2(2000) field.  Perhaps
>something such as "description varchar2(2000)" could be
>added to NAFeature?  The NAFeature view is really hurting
>for a field to store a long string of text.
>
>  
>
>>I think that you are right about the need for taxon_id. Note that it
>>should probably go in AASequenceImp (the table) and be inherited by all
>>views. Anyone have a problem with that for GUS 3.5?
>>    
>>
>
>I agree that that is the right way to do it.  Sometimes
>I mistakenly use the word table, when I mean view.
>
>Thanks, Josef
>
>  
>
>>Note that both AASequence and ExternalAASequence are views with
>>AASequence as the "superclass" view. external_database_release_id is a
>>named attribute of the parent table and so is inherited by all views.
>>
>>Cheers,
>>Chris
>>
>>On Jan 25, 2005, at 3:15 PM, ju...@cs... wrote:
>>
>>    
>>
>>>I recently began working with the DoTS.ExternalAASequence table for
>>>the first time, and I noticed several discrepancies with this
>>>table and the DoTS.ExternalNASequence and DoTS.NASequence tables,
>>>one of which I feel is serious.
>>>
>>>                   name            taxon_id    description   
>>>external_database_release_id
>>>                   varchar2(255)   number(12)  varchar2(2000)
>>>number(10)
>>>
>>>ExternalNASequence  yes            yes         yes              yes
>>>NASequence          no             yes         yes              no
>>>ExternalAASequence  yes            no          yes              yes
>>>AASequence          no             no          yes              yes
>>>
>>>
>>>      
>>>
>>[...]
>>    
>>
>
>
>
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>  
>

Re: [Gusdev-gusdev] Inconsistency among Sequence tables

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

Josef-

Thanks for bringing up all these points.

An answer to how AASequence has gone so long without taxon id is that 
historically, we have used proteins mostly in relationship to or 
translated from NASequences. But, clearly, they should have a taxon_id.

Another place to look for schema issues is:
http://gusdb.org/wiki/index.php/GusFourPointOhIdeas

That page describes proposals being generated by a work-in-progress 
internal committee that is reviewing the schema for gus 4.0. You'll 
notice there that for 4.0 the proposal is to lose the distinction 
between internal and external sequences, making all sequences 
potentially external.

steve

Chris Stoeckert wrote:

> Hi Josef,
> Your comments are very timely in light of our plans to release GUS 3.5 
> shortly which is meant to address issues such as you raise. Mike sent 
> mail earlier today on this but please see 
> http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>
> I think that you are right about the need for taxon_id. Note that it 
> should probably go in AASequenceImp (the table) and be inherited by 
> all views. Anyone have a problem with that for GUS 3.5?
>
> Note that both AASequence and ExternalAASequence are views with 
> AASequence as the "superclass" view. external_database_release_id is a 
> named attribute of the parent table and so is inherited by all views.
>
> Cheers,
> Chris
>
> On Jan 25, 2005, at 3:15 PM, ju...@cs... wrote:
>
>>
>> I recently began working with the DoTS.ExternalAASequence table for
>> the first time, and I noticed several discrepancies with this
>> table and the DoTS.ExternalNASequence and DoTS.NASequence tables,
>> one of which I feel is serious.
>>
>> name taxon_id description external_database_release_id
>> varchar2(255) number(12) varchar2(2000) number(10)
>>
>> ExternalNASequence yes yes yes yes
>> NASequence no yes yes no
>> ExternalAASequence yes no yes yes
>> AASequence no no yes yes
>>
>>
>> Looking at the above chart, we see that both AASequence
>> and ExternalAASequence lack the taxon_id. This surely must
>> be an oversight, I cannot imagine why such a thing
>> could be intentional.
>>
>> A minor annoyance is that NASequence and AASequence lack a
>> "name varchar2(255)" column and therefore must have all text
>> regarding a sequence in the description column. For query
>> and display purposes, it is very useful to be
>> able to refer to a sequence by a shorter handle.
>>
>> And a final odd observation: why does AASequence have
>> a external_database_release_id column? If an AA sequence belongs
>> to an external database, then it should be in the ExternalAASequence
>> table.
>>
>> First, I wonder how the lack of a taxon_id column in the
>> ExternalAASequence/AASequence tables has existed for so long.
>> Have these tables not been used much by the GUS community?
>>
>> Second, I wonder if the maintainers of GUS are interested
>> in addressing this issue and possibly resolving these
>> discrepancies in a future GUS release.
>>
>> I am using Version 3.0 of the schema.
>>
>>
>> Thanks, 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
>>
>>
>>
>>
>>
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>
>
>
>
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Re: [Gusdev-gusdev] GUS 3.5 Release

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

On Jan 26, 2005, at 11:36 AM, Chris Stoeckert wrote:

> Can you post the CDAT schema?

Happy to, although it will make more sense in the context of a 
presentation on it's specific design goals and use cases.

Re: [Gusdev-gusdev] GUS 3.5 Release

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

Aaron,
Sounds good. Can you post the CDAT schema? Do you think we should be 
thinking of a phylo/evo schema (in the sense of DoTS, RAD, etc.) 
instead of just adding tables. views to DoTS?

Mind you, we don't want to derail GUS3.5 release with major changes. 
That's for 4.0. I'm thinking of either sliding in a table or two if 
that works for 3.5 but keeping an eye out for needed changes for 4.0.

Cheers,
Chris

On Jan 26, 2005, at 11:22 AM, Aaron J. Mackey wrote:

>
> On Jan 26, 2005, at 11:13 AM, Michael Saffitz wrote:
>
>> GUS doesn't currently support phylogeny/evolutionary data, but are 
>> very open to adding it to GUS.  Do you have a schema (rough or 
>> otherwise) in mind?
>
> I think the upcoming comparative genomics efforts here (and elsewhere) 
> will certainly require support for evolutionary analyses.  I would 
> encourage those doing the schema design to consider both multiple 
> sequence alignments and trees (including associated bootstraps, 
> likelihood, branch lengths, etc) as experimental results that may be 
> computed in many different fashions.  I.e. don't fall into the trap of 
> the "one true tree", because it doesn't exist.
>
> I'd be very interested to be involved in this effort, and to give a 
> talk on my own phylogenetic sequence database (CDAT) for consideration 
> as one possible schema to mimic.
>
> -Aaron
>
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  am...@pc...
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
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Re: [Gusdev-gusdev] GUS 3.5 Release

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

On Jan 26, 2005, at 11:13 AM, Michael Saffitz wrote:

> GUS doesn't currently support phylogeny/evolutionary data, but are 
> very open to adding it to GUS.  Do you have a schema (rough or 
> otherwise) in mind?

I think the upcoming comparative genomics efforts here (and elsewhere) 
will certainly require support for evolutionary analyses.  I would 
encourage those doing the schema design to consider both multiple 
sequence alignments and trees (including associated bootstraps, 
likelihood, branch lengths, etc) as experimental results that may be 
computed in many different fashions.  I.e. don't fall into the trap of 
the "one true tree", because it doesn't exist.

I'd be very interested to be involved in this effort, and to give a 
talk on my own phylogenetic sequence database (CDAT) for consideration 
as one possible schema to mimic.

-Aaron

--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  am...@pc...
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

Re: [Gusdev-gusdev] GUS 3.5 Release

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

Hi Alberto and all,

I'm replying to my own post here, after speaking with Chris and Steve 
here.  GUS doesn't currently support phylogeny/evolutionary data, but 
are very open to adding it to GUS.  Do you have a schema (rough or 
otherwise) in mind?

--Mike


Michael Saffitz wrote:
> 
> Hi Alberto,
> 
> My comments are below...
> 
> 
> Alberto Davila wrote:
> 
>> Hi Mike,
>>
>> I have 3 questions for you:
>>
>> a) Such as Sucheta, I wonder we will be able to move from GUS 3.0 to 3.5
>> without big problems
>>
> 
> Yes, in short.  See my previous email to Sucheta and the list with more 
> details.
> 
>> b) Will 3.5 support (be compatible) with Postgres ? That would be bad to
>> have to debug/port it "again" to Postgres..
>>
> 
> Yes, official PostgreSQL support is a major enhancement to GUS in 3.5. 
> It's worth noting:  GUS _does not_ currently support Postgres.  The work 
> that has been done and released was very preliminary work, provided 
> because there were many groups out there who absolutely needed something 
> ASAP.  The Postgres support in 3.5 will be different than what was 
> previously sent by me-- it more closely resembles the last round of 
> scripts sent by Jeetendra.
> 
>> c) I went to the wiki site you mentioned, but was unable to enter/open
>> the BrowseSchema, so... will 3.5 support or have tables for
>> phylogeny/evolutionary data (distance, maximum likelihood and
>> bayesian)  ?
> 
> 
> Sorry about that-- the SchemaBrowser linked from those pages is now 
> working.  I'm not aware of any additional tables for this type of data, 
> perhaps someone more knowledgeable with this can let the list know if 
> tables to support this data already exist?
> 
> --Mike
> 
>>
>> Thanks, Alberto
>>
>> On Tue, 2005-01-25 at 11:15 -0500, Michael Saffitz wrote:
>>
>>> All,
>>>
>>> As you may be aware, we've been working towards a GUS 3.5 release for 
>>> quite some time now.  There is now a wiki page, available at:
>>>
>>> http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>>>
>>> which outlines the major changes that are planned for GUS 3.5.  These 
>>> items are the result of many conversations here at CBIL and with our 
>>> collaborators.
>>>
>>> 3.5 is primarily intended to be a maintenance release, to be 
>>> eventually followed with 4.0 which will be a major feature release.  
>>> Having said that, we're interested in feedback on any (high priority) 
>>> pressing issues that have been omitted from the road map above and 
>>> should be considered for 3.5.
>>>
>>> Thanks,
>>>
>>> Mike Saffitz
>>
>>
>>
>>
>>
>>
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>> Tool for open source databases. Create drag-&-drop reports. Save time
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>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> 
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Re: [Gusdev-gusdev] GUS 3.5 Release

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

Hi Alberto,

My comments are below...


Alberto Davila wrote:
> Hi Mike,
> 
> I have 3 questions for you:
> 
> a) Such as Sucheta, I wonder we will be able to move from GUS 3.0 to 3.5
> without big problems
> 

Yes, in short.  See my previous email to Sucheta and the list with more 
details.

> b) Will 3.5 support (be compatible) with Postgres ? That would be bad to
> have to debug/port it "again" to Postgres..
> 

Yes, official PostgreSQL support is a major enhancement to GUS in 3.5. 
It's worth noting:  GUS _does not_ currently support Postgres.  The work 
that has been done and released was very preliminary work, provided 
because there were many groups out there who absolutely needed something 
ASAP.  The Postgres support in 3.5 will be different than what was 
previously sent by me-- it more closely resembles the last round of 
scripts sent by Jeetendra.

> c) I went to the wiki site you mentioned, but was unable to enter/open
> the BrowseSchema, so... will 3.5 support or have tables for
> phylogeny/evolutionary data (distance, maximum likelihood and
> bayesian)  ?

Sorry about that-- the SchemaBrowser linked from those pages is now 
working.  I'm not aware of any additional tables for this type of data, 
perhaps someone more knowledgeable with this can let the list know if 
tables to support this data already exist?

--Mike

> 
> Thanks, Alberto
> 
> On Tue, 2005-01-25 at 11:15 -0500, Michael Saffitz wrote:
> 
>>All,
>>
>>As you may be aware, we've been working towards a GUS 3.5 release for 
>>quite some time now.  There is now a wiki page, available at:
>>
>>http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>>
>>which outlines the major changes that are planned for GUS 3.5.  These 
>>items are the result of many conversations here at CBIL and with our 
>>collaborators.
>>
>>3.5 is primarily intended to be a maintenance release, to be eventually 
>>followed with 4.0 which will be a major feature release.  Having said 
>>that, we're interested in feedback on any (high priority) pressing 
>>issues that have been omitted from the road map above and should be 
>>considered for 3.5.
>>
>>Thanks,
>>
>>Mike Saffitz
> 
> 
> 
> 
> 
> -------------------------------------------------------
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> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
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Re: [Gusdev-gusdev] GUS 3.5 Release

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

Hi Sucheta,

First, a quick clarification:  GUS 3.5 has _not_ been released yet. 
This is purely an announcement and solicitation for feedback.  We expect 
to release GUS 3.5 in mid-February.

We do plan on providing upgrade scripts to GUS 3.5.  The major problem 
here is that our versioning in the past has not been very strict, so 
these scripts will need to be manually applied and reviewed.  With the 
GUS 3.5 release, we will be including a XML version of the schema, which 
will allow for proper upgrading in the future, including the possibility 
of automated upgrades.

--Mike




Sucheta Tripathy wrote:
> Hi Mike,
> 
> Its great that you have released GUS 3.5. Will I be able to upgrade my
> version from 3.0 to 3.5 smoothly?
> 
> Sucheta
> 
> 
>>
>>All,
>>
>>As you may be aware, we've been working towards a GUS 3.5 release for
>>quite some time now.  There is now a wiki page, available at:
>>
>>http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>>
>>which outlines the major changes that are planned for GUS 3.5.  These
>>items are the result of many conversations here at CBIL and with our
>>collaborators.
>>
>>3.5 is primarily intended to be a maintenance release, to be eventually
>>followed with 4.0 which will be a major feature release.  Having said
>>that, we're interested in feedback on any (high priority) pressing
>>issues that have been omitted from the road map above and should be
>>considered for 3.5.
>>
>>Thanks,
>>
>>Mike Saffitz
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
>>Tool for open source databases. Create drag-&-drop reports. Save time
>>by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
>>Download a FREE copy at http://www.intelliview.com/go/osdn_nl
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
> 
> 
> 

Re: [Gusdev-gusdev] GUS 3.5 Release

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

Hi Mike,

I have 3 questions for you:

a) Such as Sucheta, I wonder we will be able to move from GUS 3.0 to 3.5
without big problems

b) Will 3.5 support (be compatible) with Postgres ? That would be bad to
have to debug/port it "again" to Postgres..

c) I went to the wiki site you mentioned, but was unable to enter/open
the BrowseSchema, so... will 3.5 support or have tables for
phylogeny/evolutionary data (distance, maximum likelihood and
bayesian)  ?

Thanks, Alberto

On Tue, 2005-01-25 at 11:15 -0500, Michael Saffitz wrote:
> 
> All,
> 
> As you may be aware, we've been working towards a GUS 3.5 release for 
> quite some time now.  There is now a wiki page, available at:
> 
> http://gusdb.org/wiki/index.php/Gus3.5RoadMap
> 
> which outlines the major changes that are planned for GUS 3.5.  These 
> items are the result of many conversations here at CBIL and with our 
> collaborators.
> 
> 3.5 is primarily intended to be a maintenance release, to be eventually 
> followed with 4.0 which will be a major feature release.  Having said 
> that, we're interested in feedback on any (high priority) pressing 
> issues that have been omitted from the road map above and should be 
> considered for 3.5.
> 
> Thanks,
> 
> Mike Saffitz