gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] GUS 3.5 Release

[Sucheta T. <su...@vb...>]

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
>
>
>
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> Tool for open source databases. Create drag-&-drop reports. Save time
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-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] Inconsistency among Sequence tables

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

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
> >
> >
> [...]

Re: [Gusdev-gusdev] Inconsistency among Sequence tables

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

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
>
>
>
>
>
> -------------------------------------------------------
> 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] Inconsistency among Sequence tables

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

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

[Gusdev-gusdev] GUS 3.5 Release

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

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

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

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

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
>>>
>>>
>
>
>
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>

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

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

Hi Dave,

We have been debugging WDK 1.1 with the Postgres version of GUS and we
aim to send back our modifications/comments to "gusdev" as soon as
possible... meanwhile, some further potential errors:

WDK Toysite is apparently installed ... in the manual (wiki) there are
several tests to be done by command line: wdkXml, wdkQuery, wdkRecord,
wdkSummary e wdkSanityTest.

By running "wdkXml" we got the output listed below... is it ok ?

[poliana@phytomonas gus_home]$ wdkXml -model toyModel 
WdkModel: name='toyModel'
displayName='GUS Web Development Kit Demo'
introduction='Welcome to WDKToySite, a sample website driven by the
GUS Web Development Kit.        You are invited to explore this site
to find out about the core functionalities of WDK.        Enjoy the
surfing!'
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooo Param Sets oooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
 
=========================== params ===============================
 
ParamSet: name='params'
 
:::::::::::::::::::::::::::::::::::::::::::::
org.gusdb.wdk.model.StringParam: name='primaryKey'
  prompt='Primary Key'
  help='primary key'
  default='null'
  sample='null'
  regex='null'
  substitute='false'
 
:::::::::::::::::::::::::::::::::::::::::::::
org.gusdb.wdk.model.FlatVocabParam: name='EstLib'
  prompt='EST Library'
  help='Library from which EST originate'
  default='null'
 
 
:::::::::::::::::::::::::::::::::::::::::::::
org.gusdb.wdk.model.FlatVocabParam: name='ApiTaxon'
  prompt='Organism'
  help='Apicomplexon taxons'
  default='null'
 
 
:::::::::::::::::::::::::::::::::::::::::::::
org.gusdb.wdk.model.StringParam: name='NumEstLibs'
  prompt='Number of EST Libs'
  help='number of distinct libs'
  default='null'
  sample='3'
  regex='\d+'
  substitute='false'

:::::::::::::::::::::::::::::::::::::::::::::
org.gusdb.wdk.model.StringParam: name='NumSeqs'
  prompt='Number of Contained Sequences'
  help='number of seqs'
  default='null'
  sample='null'
  regex='\d+'
  substitute='false'

:::::::::::::::::::::::::::::::::::::::::::::
org.gusdb.wdk.model.StringParam: name='AssemblyConsistency'
  prompt='Assembly consistency score'
  help='on the scale of 0-100'
  default='null'
  sample='95'
  regex='100|\d|\d{2}'
  substitute='false'



ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooo Query Sets oooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

=========================== VocabQueries ===============================

QuerySet: name='VocabQueries'

:::::::::::::::::::::::::::::::::::::::::::::
Query: name='EstLib'
  displayName='EstLib'
  description='null'
  help='null'
  sql='select distinct dbest_name as term, library_id as internal     
          from WDKTestLibrary'
--- Columns ---
org.gusdb.wdk.model.Column: name='term'
  displayName='null'
  help='null'
  dataTypeName='null'
  inSummary='true'

org.gusdb.wdk.model.Column: name='internal'
  displayName='null'
  help='null'
  dataTypeName='null'
  inSummary='true'

--- Params ---


:::::::::::::::::::::::::::::::::::::::::::::
Query: name='ApiTaxon'
  displayName='ApiTaxon'
  description='null'
  help='null'
  sql='select distinct name as term, taxon_id as internal             
  from WDKTestTaxonName                where name in ('Neospora
caninum', 'Plasmodium falciparum', 'Eimeria tenella',                 
             'Plasmodium yoelii', 'Sarcocystis neurona', 'Toxoplasma
gondii')'
--- Columns ---
org.gusdb.wdk.model.Column: name='term'
  displayName='null'
  help='null'
  dataTypeName='null'
  inSummary='true'

org.gusdb.wdk.model.Column: name='internal'
  displayName='null'
  help='null'
  dataTypeName='null'
  inSummary='true'

--- Params ---


=========================== RnaAttributes
===============================

QuerySet: name='RnaAttributes'

:::::::::::::::::::::::::::::::::::::::::::::
Query: name='AssemblyAttrs'
  displayName='AssemblyAttrs'
  description='null'
  help='null'
  sql='select a.assembly_consistency,                       
a.contains_mrna,                       a.number_of_contained_sequences
               from WDKTestAssembly a, WDKTestTaxonName tn            
    where a.na_sequence_id = $$primaryKey$$
             and a.taxon_id = tn.taxon_id'
--- Columns ---
org.gusdb.wdk.model.Column: name='assembly_consistency'
  displayName='Assembly consistency'
  help='null'
  dataTypeName='null'
  inSummary='true'

org.gusdb.wdk.model.Column: name='contains_mrna'
  displayName='Contains mRNA'
  help='null'
  dataTypeName='null'
  inSummary='true'

org.gusdb.wdk.model.Column: name='number_of_contained_sequences'
  displayName='Number contained sequences'
  help='null'
  dataTypeName='null'
  inSummary='true'

The remining output is pretty similar...

The next (tests) commands are showing some output errors:

[poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
RnaIds.ByDbESTLib  -params NumEstLibs 6 ApiTaxon "Neospora caninum"
 
'ApiTaxon' is not a legal parameter name for query 'RnaIds.ByDbESTLib'

Any tips/suggestions ?

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

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] Problem building WDK on Fedora

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

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] Problem building WDK on Fedora

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

Forgot to mention that because the "Permission denied" error, we changed 
the permissions but the error remains the same...

Alberto


At 17:41 18/1/2005, 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] error when loading nrdb

[John I. <io...@pc...>]

Marc,

In this case, when you're adding a new database release to your GUS
instance, it will be necessary to add a new record to the
SRes.ExternalDatabaseRelease table.  If this is the first time NRDB has
been loaded into your instance, you must also create a record for NRDB
in SRes.ExternalDatabase.  Both records can be created with the
UpdateGUSFromXML plugin.

First, check to see if there's already an NRDB record in
ExternalDatabase.  If there isn't you can create one by giving this XML
to UpdateGUSFromXML:

<SRes::ExternalDatabase>
  <name>NRDB</name>
  <lowercase_name>nrdb</lowercase_name>
</SRes::ExternalDatabase>

Once you have found or created the ExternalDatabase record for NRDB,
plug its external_database_release_id ("123" in this example) into this:

<SRes::ExternalDatabaseRelease>
  <external_database_id>123</external_database_id>
  <release_date>2005-01-18 00:00:00</release_date>
  <version>continuous</version>
  <id_type>accession</id_type>
  <description>Non-redundant composite of protein data</description>
</SRes::ExternalDatabaseRelease>

John



On Tue, 2005-01-18 at 12:28, marc jackson wrote:
> Hi John,
> 
> I've  been looking thru the documentation.  How does one discover the
> release_ID of a database?
> 
> Regards,
> 
> Marc
> 
> 
> 
> 
> >From: io...@pc... 
> >To: marc jackson <de...@ho...> 
> >CC: gus...@li... 
> >Subject: Re: [Gusdev-gusdev] error when loading nrdb 
> >Date: Sat, 15 Jan 2005 12:48:28 -0500 
> > 
> >Marc, 
> > 
> >I wasn't familiar with the details of that plugin, so I got the
> parameter list 
> >by typing: 
> > 
> >ga GUS::Common::Plugin::LoadNRDB --help 
> > 
> >The resulting list shows that the plugin takes the
> external_database_release_id 
> >for NRDB as a command-line argument in the format --extDbRelId=i
> (where "i" is 
> >the release ID).  The message you got seems to imply that this
> argument is 
> >required (which makes sense, since NRDB is an external database and
> its records 
> >must be distinguished by release). 
> > 
> >John 
> > 
> > 
> >Quoting marc jackson <de...@ho...>: 
> > 
> > > Hello, 
> > > 
> > > Does anyone know what the following error means? 
> > > 
> > > prompt>  ga GUS::Common::Plugin::LoadNRDB --nrdb=./nr.tar.gz
> --commit 
> > > 
> > > output: 
> > > 
> > > Fri Jan 14 15:06:20 2005        ***COMMIT ON*** 
> > > 
> > > external_database_release_id not supplied\n at 
> > > /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 112.
> > > 
> > > 
> > > 
> > > ------------------------------------------------------- 
> > > The SF.Net email is sponsored by: Beat the post-holiday blues 
> > > Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
> > > It's fun and FREE -- well,
> almost....http://www.thinkgeek.com/sfshirt 
> > > _______________________________________________ 
> > > Gusdev-gusdev mailing list 
> > > Gus...@li... 
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev 
> > > 
> > 
> > 
-- 
John Iodice
Programmer/Analyst
Computational Biology and Informatics Lab
University of Pennsylvania
http://cbil.upenn.edu

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

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

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

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

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] error when loading nrdb

[<io...@pc...>]

Marc,

I wasn't familiar with the details of that plugin, so I got the parameter list
by typing:

ga GUS::Common::Plugin::LoadNRDB --help

The resulting list shows that the plugin takes the external_database_release_id
for NRDB as a command-line argument in the format --extDbRelId=i (where "i" is
the release ID).  The message you got seems to imply that this argument is
required (which makes sense, since NRDB is an external database and its records
must be distinguished by release).

John


Quoting marc jackson <de...@ho...>:

> Hello,
>
> Does anyone know what the following error means?
>
> prompt>  ga GUS::Common::Plugin::LoadNRDB --nrdb=./nr.tar.gz --commit
>
> output:
>
> Fri Jan 14 15:06:20 2005        ***COMMIT ON***
>
> external_database_release_id not supplied\n at
> /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 112.
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by: Beat the post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
> It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] error when loading nrdb

[marc j. <de...@ho...>]

<html><div style='background-color:'><DIV class=RTE>Hello,</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>Does anyone know what the following error means?</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>prompt&gt;&nbsp; ga GUS::Common::Plugin::LoadNRDB --nrdb=./nr.tar.gz --commit</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>output:</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>Fri Jan 14 15:06:20 2005&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ***COMMIT ON***</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>external_database_release_id not supplied\n at /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 112.</DIV></div></html>

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

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

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] Problem building WDK on Fedora

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

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

[Gusdev-gusdev] dots.rnatype view definition

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

Ed Robinson noticed another feature with a faulty definition so being in 
the mode I have modified the SQL and this will be used in our instance 
of GUS and in GUS 3.5:

SELECT na_feature_id,
na_sequence_id,
subclass_view,
name
sequence_ontology_id,
parent_id,
external_database_release_id,
source_id,
prediction_algorithm_id,
is_predicted,
review_status_id,
string1 as anticodon,
string2 as citation,
string3 as codon,
string4 as evidence,
string5 as function,
string6 as gene,
string7 as label,
string8 as map,
string9 as partial,
string10 as product,
string11 as pseudo,
string12 as standard_name,
string13 as usedin,
tinyint1 as is_partial,
tinyint2 as is_pseudo,
modification_date,
user_read,
user_write,
group_read,
group_write,
other_read,
other_write,
row_user_id,
row_group_id,
row_project_id,
row_alg_invocation_id,
FROM NAFeatureImp WHERE subclass_view = 'RNAType' WITH CHECK OPTION

[Gusdev-gusdev] dots.rnatype

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

Ed Robinson noticed another feature with a faulty definition so being in 
the mode I have modified the SQL and this will be used in our instance 
of GUS and in GUS 3.5:

SELECT na_feature_id,
na_sequence_id,
subclass_view,
name
sequence_ontology_id,
parent_id,
external_database_release_id,
source_id,
prediction_algorithm_id,
is_predicted,
review_status_id,
string1 as anticodon,
string2 as citation,
string3 as codon,
string4 as evidence,
string5 as function,
string6 as gene,
string7 as label,
string8 as map,
string9 as partial,
string10 as product,
string11 as pseudo,
string12 as standard_name,
string13 as usedin,
tinyint1 as is_partial,
tinyint2 as is_pseudo,
modification_date,
user_read,
user_write,
group_read,
group_write,
other_read,
other_write,
row_user_id,
row_group_id,
row_project_id,
row_alg_invocation_id,
FROM NAFeatureImp WHERE subclass_view = 'RNAType' WITH CHECK OPTION

[Gusdev-gusdev] dots.transcript view definition

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

The view defintion for dots.transcript and dotsver.transcriptver does 
not conform to the superclass. The SQL will be altered within our 
instance and incorporated into GUS 3.5 as the following:  
(dotsver.transcriptver should correspond to this query)

SELECT na_feature_id,
na_sequence_id,
subclass_view,
name,
sequence_ontology_id,
parent_id,
external_database_release_id,
source_id,
prediction_algorithm_id,
is_predicted,
review_status_id,
string1 as citation,
string2 as clone,
string3 as codon,
int1 as codon_start,
string4 as cons_splice,
string5 as ec_number,
string6 as evidence,
string7 as function,
string8 as gene,
string9 as label,
string10 as map,
string11 as num,
string12 as partial,
string13 as product,
string14 as protein_id,
string15 as pseudo,
string16 as standard_name,
text1 as translation,
string17 as transl_except,
int2 as transl_table,
string18 as usedin,
tinyint1 as is_partial,
tinyint2 as is_pseudo,
modification_date,
user_read,
user_write,
group_read,
group_write,
other_read,
other_write,
row_user_id,
row_group_id,
row_project_id,
row_alg_invocation_id,
FROM NAFeatureImp WHERE subclass_view = 'Transcript' WITH CHECK OPTION

[Gusdev-gusdev] nr.tar.gz

[marc j. <de...@ho...>]

<html><div style='background-color:'><DIV class=RTE>Hello,</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>In the installation documentation, there is a segment for downloading <A href="ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz">ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz</A>.&nbsp; How do I get this information </DIV>
<DIV class=RTE>into the GUS database?</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>i.e. there should be a ga GUS::Common::Plugin::SubmitRow --tablename *, but I don't see that information.&nbsp; How is nr.gz actually used?</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>Regards,</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>Marc</DIV></div></html>

Re: [Gusdev-gusdev] Re: problems building gus on redhat linux

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

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
> &gt;&gt;------------------------------------------------------- SF email is
> &gt;&gt;sponsored by - The IT Product Guide Read honest &amp; candid reviews
> on
> &gt;&gt;hundreds of IT Products from real users. Discover which products
> &gt;&gt;truly live up to the hype. Start reading now.
> &gt;&gt;http://productguide.itmanagersjournal.com/
> &gt;&gt;_______________________________________________ Gusdev-gusdev
> &gt;&gt;mailing list Gusdev-gusdev@li...
> &gt;&gt;https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> &gt;
>
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by: Beat the post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
> It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] wdk classic help!!

[<jjh...@vb...>]

Sucheta,

You need to set following environment variables in your httpd.conf.
Assuming that you are using cgi-bin directory, you http.conf entry should
look something like this:

<Directory "/usr/local/apache2/cgi-bin">
    AllowOverride AuthConfig
    Options None
    Order allow,deny
    Allow from all
    SetEnv ORACLE_BASE /home/oracle
    SetEnv ORACLE_HOME /home/oracle/OraHome1
    SetEnv ORACLE_SID  GUS
    SetEnv NSL_LANG    AMERICAN_AMERICA.US7ASCII
</Directory>

>
> Hi,
>
> I know its no longer supported, but I will appreciate if anyone can tell
> me how to solve this problem.
>
> I am using the WDK classic , things seem to be OK. But for the graphics,
> @SCRIPT_DIR@ scripts don't work. In the error_log file I get error saying:
>
> check ORACLE_HOME NLS setting etc.
>
> Eventhough I have set the $ORACLE_HOME environment variable correctly
>
> Any ideas?
>
> many thanks
>
> Sucheta
>
>
> --
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by: Beat the post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
> It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] wdk classic help!!

[Sucheta T. <su...@vb...>]

Hi,

I know its no longer supported, but I will appreciate if anyone can tell
me how to solve this problem.

I am using the WDK classic , things seem to be OK. But for the graphics,
@SCRIPT_DIR@ scripts don't work. In the error_log file I get error saying:

check ORACLE_HOME NLS setting etc.

Eventhough I have set the $ORACLE_HOME environment variable correctly

Any ideas?

many thanks

Sucheta


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

[Gusdev-gusdev] RES: problems building gus on redhat linux

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

SSB3YXMgdHJ5aW5nIHRvIGluc3RhbGwgdGhlIFdESyAxLjEsIHRoZSBzb2Z0d2FyZXMvc3lzdGVt
IHdlIGFyZSB1c2luZyBpczoNCiANCkFudDogYXBhY2hlLWFudC0xLjYuMg0KVG9tQ2F0OiBqYWth
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bmcgZ3VzIG9uIHJlZGhhdCBsaW51eA0KCQ0KCQ0KCSANCg0K

[Gusdev-gusdev] Re: problems building gus on redhat linux

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

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
=20
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 =20
2004-12-17 10:21

 That wasn"t it, but things are resolved.  For now. :)
=20
 Thanks for your help!
=20
 Regards,
=20
 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=20
 &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
 &gt;&gt;------------------------------------------------------- SF =
email is
 &gt;&gt;sponsored by - The IT Product Guide Read honest &amp; candid =
reviews=20
 on
 &gt;&gt;hundreds of IT Products from real users. Discover which =
products
 &gt;&gt;truly live up to the hype. Start reading now.
 &gt;&gt;http://productguide.itmanagersjournal.com/
 &gt;&gt;_______________________________________________ Gusdev-gusdev
 &gt;&gt;mailing list Gusdev-gusdev@li...
 &gt;&gt;https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
 &gt;
=20