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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