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

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

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

Alberto


At 17:41 18/1/2005, Alberto Davila wrote:
>Thanks Steve !
>
>We managed to pass that error.
>
>Now, when trying "
>wdkRegressionTest":
>
>[poliana@phytomonas gus_home]$ wdkRegressionTest
>--commandListFile=/usr/local/GUS/gus_home/data/WDKToySite/Model/regressionTest/sampleRegressionTestCommands
>
>running regression test newCacheTest
>
>sh: line 1: /newCacheTest.out: Permission denied
>diff: /newCacheTest.out: No such file or directory
>diff:
>/usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/newCacheTest.out:
>No such file or directory
>
>Error!  Test newCacheTest failed!
>The observed result of the test was different than the expected result
>of a test previously run.
>To see the difference, run diff /newCacheTest.out
>/usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/newCacheTest.out
>
>Received error in critical test newCacheTest.  Ending regression test
>at /usr/local/GUS/gus_home/bin/wdkRegressionTest line 115, <GEN0> line
>3.
>
>
>Is the path "
>/usr/local/GUS/gus_home/data/WDK/ToyModel/regressionTest/expectedResult/newCacheTest.out" 
>correct ? Just realized we have this PATH: 
>"/usr/local/GUS/gus_home/data/WDKToySite/Model/regressionTest" instead.
>
>
>Regards, Alberto
>
>
>At 20:44 17/1/2005, Steve Fischer wrote:
>>i think the problem is that we have the oracle driver hard coded.
>>
>>take a look in $PROJECT_HOME/WDK/Model/bin/wdkCache.
>>
>>my $cmd = "java -Djdbc.drivers=oracle.jdbc.driver.OracleDriver 
>>-DconfigDir=$GUS_HOME/config -DcmdName=wdkCache -classpath $CLASSPATH 
>>org.gusdb.wdk.model.ResultFactory $args";
>>
>>as a workaround, in the files in that directory, change to postgres drivers.
>>
>>we'll make it configurable.
>>
>>you'll also need to write a new class for postrgres.
>>
>>the Oracle version is:
>>
>>$PROJECT_HOME/WDK/Model/src/java/org/gusdb/wdk/model/implementation/Oracle.java
>>
>>you'll need to make a similar class for postgres.   then, in the file 
>>$PROJECT_HOME/WDKToySite/Model/config/toyModel-config.xml
>>
>>you'll need to refer to that class:
>><modelConfig login="yourLoginHere"
>>         password="yourPasswordHere"
>>         connectionUrl="yourConnectionUrlHere"
>>         queryInstanceTable="QueryInstance"
>>         maxQueryParams="50"
>>         platformClass="org.gusdb.wdk.model.implementation.Oracle"
>>             initialSize="3"
>>             maxActive="20"
>>             maxIdle="3"
>>             minIdle="3"
>>             maxWait="500"/>
>>
>>
>>
>>Alberto Davila wrote:
>>
>>>Hi Dave,
>>>
>>>You are right... that output seem to be fine... however we cannot use 
>>>WDK, here are more logs:
>>>
>>>[poliana@phytomonas gus_home]$ wdkCache -model toyModel -new
>>>
>>>Making cache table gus.QueryInstance
>>>
>>>Failed executing sql:
>>>create table gus.QueryInstance (query_instance_id number(12) not null,
>>>query_name varchar2(100) not null, cached number(1) not
>>>null,result_table varchar2(30), start_time date not null, end_time
>>>date, dataset_name varchar2(100), session_id varchar2(50), param0
>>>varchar2(200), param1 varchar2(200), param2 varchar2(200), param3
>>>varchar2(200), param4 varchar2(200), param5 varchar2(200), param6
>>>varchar2(200), param7 varchar2(200), param8 varchar2(200), param9
>>>varchar2(200), param10 varchar2(200), param11 varchar2(200), param12
>>>varchar2(200), param13 varchar2(200), param14 varchar2(200), param15
>>>varchar2(200), param16 varchar2(200), param17 varchar2(200), param18
>>>varchar2(200), param19 varchar2(200), param20 varchar2(200), param21
>>>varchar2(200), param22 varchar2(200), param23 varchar2(200), param24
>>>varchar2(200), param25 varchar2(200), param26 varchar2(200), param27
>>>varchar2(200), param28 varchar2(200), param29 varchar2(200), param30
>>>varchar2(200), param31 varchar2(200), param32 varchar2(200), param33
>>>varchar2(200), param34 varchar2(200), param35 varchar2(200), param36
>>>varchar2(200), param37 varchar2(200), param38 varchar2(200), param39
>>>varchar2(200), param40 varchar2(200), param41 varchar2(200), param42
>>>varchar2(200), param43 varchar2(200), param44 varchar2(200), param45
>>>varchar2(200), param46 varchar2(200), param47 varchar2(200), param48
>>>varchar2(200), param50 varchar2(200))
>>>
>>>FAILED
>>>
>>>org.gusdb.wdk.model.WdkModelException: java.sql.SQLException: No 
>>>suitable driver
>>>         at 
>>> org.gusdb.wdk.model.ResultFactory.createCache(ResultFactory.java:136)
>>>         at org.gusdb.wdk.model.ResultFactory.main(ResultFactory.java:524)
>>>Caused by: java.sql.SQLException: No suitable driver
>>>         at java.sql.DriverManager.getConnection(DriverManager.java:532)
>>>         at java.sql.DriverManager.getConnection(DriverManager.java:171)
>>>         at 
>>> org.apache.commons.dbcp.DriverManagerConnectionFactory.createConnection(DriverManagerConnectionFactory.java:94) 
>>>
>>>         at 
>>> org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:300) 
>>>
>>>         at 
>>> org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:816) 
>>>
>>>         at 
>>> org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:140) 
>>>
>>>         at 
>>> org.gusdb.wdk.model.implementation.SqlUtils.execute(SqlUtils.java:206)
>>>         at 
>>> org.gusdb.wdk.model.ResultFactory.createCache(ResultFactory.java:127)
>>>         ... 1 more
>>>
>>>
>>>We have the Postgres JDBC installed and its PATH (export 
>>>CLASSPATH=/usr/local/GUS/gus_home/lib/java/pg74.215.jdbc3.jar) properly 
>>>set (such as stated in the manual, we have choosen the JDBC version 
>>>based on jsdk and postgres installed versions), then decided to make a 
>>>test with the JDBC (just in case...) :
>>>
>>>[poliana@phytomonas gus_home]$ java -classpath . HelloPostgresql banco
>>>user 'senha'
>>>hello
>>>
>>>Connection to PostgreSQL 7.4.6 successful.
>>>
>>>Executing this command: create table jdbc_demo (code int, text varchar(20))
>>>
>>>Executing this command: insert into jdbc_demo values (1,'One')
>>>
>>>Executing this command twice: insert into jdbc_demo values (3,'Four')
>>>
>>>Executing this command: update jdbc_demo set text = 'Three' where code = 3
>>>
>>>2 rows were update by this statement
>>>
>>>
>>>
>>>Now demostrating a prepared statement...
>>>The Statement looks like this: insert into jdbc_demo values (?,?)
>>>
>>>Looping three times filling in the fields...
>>>
>>>10...
>>>
>>>11...
>>>
>>>12...
>>>
>>>Now executing the command: select * from jdbc_demo
>>>code = 1; text = One
>>>
>>>code = 3; text = Three
>>>
>>>code = 3; text = Three
>>>
>>>code = 10; text = HiHo
>>>
>>>code = 11; text = HiHo
>>>
>>>code = 12; text = HiHo
>>>
>>>Executing this command: drop table jdbc_demo
>>>
>>>Could it be that the command "wdkCache -model toyModel -new" is trying 
>>>to build the WDK based on the "Oracle version of GUS" ? We are using the 
>>>Postgres version built with the scripts from Jeetendra...
>>>
>>>Thanks in advance for any further help ;-)
>>>
>>>Cheers, Alberto
>>>
>>>
>>>
>>>At 12:50 13/1/2005, Dave Barkan wrote:
>>>
>>>>Hi Alberto,
>>>>
>>>>The output that you sent is actually fine!  There are no error messages 
>>>>that I can see, and the output indicates that you built 
>>>>successfully.  The "no existing files, doing nothing" message is a 
>>>>simple statement that shouldn't concern you.
>>>>
>>>>Are there any other symptoms that lead you to believe there is a 
>>>>problem with the build?
>>>>
>>>>Dave
>>>>
>>>>On Thu, 13 Jan 2005, Alberto Davila wrote:
>>>>
>>>>>HI Dave,
>>>>>
>>>>>Thanks...
>>>>>
>>>>>I think we made a mistake trying to build "GUS" instead the 
>>>>>"WDKToySite", then we started again, have a look:
>>>>>
>>>>>[poliana@phytomonas gus_home]$ build WDKToySite install -append
>>>>>
>>>>>ant -f /usr/local/GUS/project_home/install/build.xml install
>>>>>-Dproj=WDKToySite -DtargetDir=/usr/local/GUS/gus_home -Dcomp=
>>>>>-DprojectsDir=/usr/local/GUS/project_home   -Dappend=true   -logger
>>>>>org.apache.tools.ant.NoBannerLogger  | grep ']'
>>>>>
>>>>>     [echo] .
>>>>>     [echo] Installing WDK/Model
>>>>>     [copy] Copying 13 files to /usr/local/GUS/gus_home/bin
>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/xml
>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/xml
>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/rng
>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/rng
>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/lib/perl/WDK/Model
>>>>>     [copy] Copying 24 files to /usr/local/GUS/gus_home/lib/perl/WDK/Model
>>>>>     [copy] Copying 10 files to /usr/local/GUS/gus_home/lib/java
>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/doc/WDK/Model
>>>>>     [copy] Copying 9 files to /usr/local/GUS/gus_home/doc/WDK/Model
>>>>>      [jar] Building jar: /usr/local/GUS/gus_home/lib/java/WDK-Model.jar
>>>>>     [echo] .
>>>>>     [echo] IMPORTANT REMINDER: If you have not already done so,
>>>>>please copy any .jar needed for database connectivity (such as
>>>>>oracle-classes12.jar) into /usr/local/GUS/gus_home/lib/java.  The WDK
>>>>>does not supply these.  See the installation instructions available at
>>>>>www.gusdb.org/wdk for details.
>>>>>     [echo] .
>>>>>     [echo] .
>>>>>     [echo] Installing WDK/Controller
>>>>>     [copy] Copying 3 files to /usr/local/GUS/gus_home/lib/java
>>>>>      [jar] Building jar: 
>>>>> /usr/local/GUS/gus_home/lib/java/WDK-Controller.jar
>>>>>     [echo] .
>>>>>     [echo] Installing WDK/View
>>>>>     [copy] Copying 2 files to /usr/local/GUS/gus_home/lib/java
>>>>>   [concat] No existing files and no nested text, doing nothing
>>>>>     [echo] .
>>>>>     [echo] Installing WDKToySite/Model
>>>>>     [copy] Copying 5 files to /usr/local/GUS/gus_home/config
>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/doc/WDKToySite/Model
>>>>>     [copy] Copying 1 file to /usr/local/GUS/gus_home/doc/WDKToySite/Model
>>>>>    [mkdir] Created dir: /usr/local/GUS/gus_home/data/WDKToySite/Model
>>>>>     [copy] Copying 13 files to 
>>>>> /usr/local/GUS/gus_home/data/WDKToySite/Model
>>>>>   [concat] No existing files and no nested text, doing nothing
>>>>>
>>>>>Here is our ".bashrc" file:
>>>>>
>>>>>[root@phytomonas poliana]# more .bashrc
>>>>># .bashrc
>>>>>
>>>>>PATH=$PATH:/usr/local/pgsql/bin; export PATH
>>>>>PATH=$PATH:/usr/java/j2sdk1.4.2_06/bin; export PATH
>>>>>PATH=$PATH:/usr/local/apache-ant-1.6.2/bin; export PATH
>>>>>export ANT_HOME=/usr/local/apache-ant-1.6.2
>>>>>export JAVA_HOME=/usr/java/j2sdk1.4.2_06
>>>>>export CATALINA_HOME=/usr/local/jakarta-tomcat-5.0.28
>>>>>export GUS_HOME=/usr/local/GUS/gus_home
>>>>>export PROJECT_HOME=/usr/local/GUS/project_home
>>>>>export GUS_CONFIG_FILE=$GUS_HOME/.gus.properties
>>>>>PATH=$GUS_HOME/bin:$PROJECT_HOME/install/bin:$ANT_HOME/bin:$PATH; 
>>>>>export PATH
>>>>>export PERL5LIB=/usr/local/GUS/gus_home/lib/perl
>>>>>
>>>>>Here is the software/system we are using:
>>>>>
>>>>>Ant: apache-ant-1.6.2
>>>>>TomCat: jakarta-tomcat-5.0.28
>>>>>Java: Java(TM) 2 Runtime Environment, Standard Edition (build 
>>>>>1.4.2_06-b03)
>>>>>Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
>>>>>Postgres: postgresql-7.4.6
>>>>>Perl: 5.8.3
>>>>>Fedora Core 1
>>>>>Kernel: 2.4.22-1.2199.nptl
>>>>>
>>>>>and, we are using the scripts for the "PostgreSQL" version posted by 
>>>>>Jeetendra (by the way, Jeetendra plugins are working fine, "SubmitRow" 
>>>>>went OK then just using "LoadTaxon", the load iof the latter is taking 
>>>>>more than 48 hours ... and still running...)
>>>>>
>>>>>any further suggestions to debug the WDK install ?
>>>>>
>>>>>Thanks, Alberto
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>At 13:49 10/1/2005, Dave Barkan wrote:
>>>>>
>>>>>>Hello,
>>>>>>This error message is usually indicative of the build system being 
>>>>>>unable to connect to your database instance.
>>>>>>Make sure that you have configured your $GUS_CONFIG_FILE and your 
>>>>>>environment variables as detailed in steps 5 and 9 of the GUS 
>>>>>>installation instructions at
>>>>>>http://www.gusdb.org/documentation/install-setup.html
>>>>>>Off the top of my head, that is the most likely solution to your 
>>>>>>problem, but if that doesn't work, I would suggest asking your DBA if 
>>>>>>they can think of anything regarding your local connection and 
>>>>>>database instance.
>>>>>>Dave
>>>>>>On Fri, 7 Jan 2005, davila wrote:
>>>>>>
>>>>>>>Hi Marc,
>>>>>>>We just tried to install the WDK 1.1. by using:
>>>>>>>build GUS install -append
>>>>>>>then got this errors:
>>>>>>>...
>>>>>>>    [javac] 
>>>>>>> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFamilyExperiment_Table.java:24: 
>>>>>>> illegal start of expression
>>>>>>>    [javac]         tableAtts.put("modification_date", new 
>>>>>>> GUSTableAttribute("modification_date", "date", 
>>>>>>> "java.lang.notdefyet", -1, , -1, false, false) );
>>>>>>>    [javac]             ^
>>>>>>>    [javac] 
>>>>>>> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AAFamilyExperiment_Table.java:24: 
>>>>>>> ')' expected
>>>>>>>    [javac]         tableAtts.put("modification_date", new 
>>>>>>> GUSTableAttribute("modification_date", "date", 
>>>>>>> "java.lang.notdefyet", -1, , -1, false, false) );
>>>>>>>    [javac]                                  ^
>>>>>>>    [javac] 100 errors
>>>>>>>BUILD FAILED
>>>>>>>/usr/local/GUS/project_home/install/build.xml:26: The following 
>>>>>>>error occurred while executing this line:
>>>>>>>/usr/local/GUS/project_home/GUS/build.xml:73: The following error 
>>>>>>>occurred while executing this line:
>>>>>>>/usr/local/GUS/project_home/install/build.xml:221: The following 
>>>>>>>error occurred while executing this line:
>>>>>>>/usr/local/GUS/project_home/install/build.xml:240: Compile failed; 
>>>>>>>see the compiler error output for details.
>>>>>>>I saw you got a similar problem and solved it. Could you kindly 
>>>>>>>share how did you solve that ?
>>>>>>>We use:
>>>>>>>Java: Java(TM) 2 Runtime Environment, Standard Edition (build 
>>>>>>>1.4.2_06-b03)
>>>>>>>Java HotSpot(TM) Client VM (build 1.4.2_06-b03, mixed mode)
>>>>>>>Apache Ant version 1.6.2 compiled on July 16 2004
>>>>>>>Thanks, Alberto
>>>>>>>
>>>>>>>
>>>>>>>From: marc jackson <dechon@ho...>
>>>>>>>Re: problems building gus on redhat linux
>>>>>>>2004-12-17 10:21
>>>>>>>That wasn"t it, but things are resolved.  For now. :)
>>>>>>>Thanks for your help!
>>>>>>>Regards,
>>>>>>>Marc
>>>>>>>&gt;From: Steve Fischer &lt;sfischer@pc...&gt;
>>>>>>>&gt;To: marc jackson &lt;dechon@ho...&gt;
>>>>>>>&gt;CC: gusdev-gusdev@li...
>>>>>>>&gt;Subject: Re: [Gusdev-gusdev] problems building gus on redhat linux
>>>>>>>&gt;Date: Fri, 17 Dec 2004 07:36:37 -0500
>>>>>>>&gt;
>>>>>>>&gt;Marc-
>>>>>>>&gt;
>>>>>>>&gt;i suspect that you haven"t defined the environment variable
>>>>>>>&gt;$GUS_CONFIG_FILE.
>>>>>>>&gt;
>>>>>>>&gt;it should be discussed in the docs.
>>>>>>>&gt;
>>>>>>>&gt;steve
>>>>>>>&gt;
>>>>>>>&gt;[sfischer@cottus ~]$ echo $GUS_CONFIG_FILE
>>>>>>>&gt;/home/sfischer/.gus.properties
>>>>>>>&gt;[sfischer@cottus ~]$ more $GUS_CONFIG_FILE
>>>>>>>&gt;databaseLogin=your_login
>>>>>>>&gt;databasePassword=your_password
>>>>>>>&gt;
>>>>>>>&gt;readOnlyDatabaseLogin=your_login
>>>>>>>&gt;readOnlyDatabasePassword=your_password
>>>>>>>&gt;
>>>>>>>&gt;dbiDsn=dbi:Oracle:host=cbilbld.pcbi.upenn.edu;sid=cbilbld
>>>>>>>#your
>>>>>>>&gt;dsn string here
>>>>>>>&gt;
>>>>>>>&gt;coreSchemaName=Core
>>>>>>>&gt;userName=sfischer     #your user name here
>>>>>>>&gt;group=CBIL     # your group name here
>>>>>>>&gt;project=GUS   # your project here
>>>>>>>&gt;[sfischer@cottus ~]$
>>>>>>>&gt;
>>>>>>>&gt;
>>>>>>>&gt;
>>>>>>>&gt;marc jackson wrote:
>>>>>>>&gt;
>>>>>>>&gt;&gt;Hello,
>>>>>>>&gt;&gt;  I"m having a problem getting GUS to install/compile. I"ve been
>>>>>>>&gt;&gt;able to configure the database, but when I go to run the
>>>>>>>&quot;ga&quot;
>>>>>>>&gt;&gt;command to bootstrap in data. it pukes.  In working with Ed
>>>>>>>&gt;&gt;Robinson, we got to the 2nd build.  Specifically:
>>>>>>>&gt;&gt;  build GUS install -append returns the following error:
>>>>>>>&gt;&gt;    [exec] Required property "group" must be specified in  at
>>>>>>>&gt;&gt;/opt/gus/gus_home/lib/perl/CBIL/Util/PropertySet.pm line 53.
>>>>>>>&gt;&gt;BUILD FAILED
>>>>>>>&gt;&gt;/opt/gus/project_home/install/build.xml:26: The following error
>>>>>>>&gt;&gt;occurred while executing this line:
>>>>>>>&gt;&gt;/opt/gus/project_home/GUS/build.xml:190: exec returned: -1
>>>>>>>&gt;&gt;  any help would be appreacited.
>>>>>>>&gt;&gt;  Regards,
>>>>>>>&gt;&gt;  Marc