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
>
>