gusdev-gusdev

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

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

Hi Dave,

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

Errors description when running "wdkQuery":

In the "PostgreSQL.java" file we edited:

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

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

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

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

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

        return "LOCALTIMESTAMP(0)";

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

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

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

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

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

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

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

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

Alberto


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

The problem with the following command

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

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

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

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

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

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

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

Let me know if there is anything else.

Thanks,
Dave


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

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

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

Hey Alberto,

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

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

Dave

On Wed, 26 Jan 2005, davila wrote:

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

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

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

Hey Alberto,

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

First of all, your assertion here:

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

The next line you mention (line 123) is

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

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

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

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

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

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

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


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

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

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

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

Abra=E7o,
Poliana


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

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

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

Folks-

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

steve

Poliana Mateus wrote:

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

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

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

Hey Folks,

OK a few thoughts on the Postgres issue.

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

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

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

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

Dave

On Fri, 28 Jan 2005, Dave Barkan wrote:

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