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Re: [Gusdev-gusdev] Problem building WDK on Fedora
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From: Alberto D. <da...@io...> - 2005-01-17 18:05:41
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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
>>>>>From: Steve Fischer <sfischer@pc...>
>>>>>To: marc jackson <dechon@ho...>
>>>>>CC: gusdev-gusdev@li...
>>>>>Subject: Re: [Gusdev-gusdev] problems building gus on redhat linux
>>>>>Date: Fri, 17 Dec 2004 07:36:37 -0500
>>>>>
>>>>>Marc-
>>>>>
>>>>>i suspect that you haven"t defined the environment variable
>>>>>$GUS_CONFIG_FILE.
>>>>>
>>>>>it should be discussed in the docs.
>>>>>
>>>>>steve
>>>>>
>>>>>[sfischer@cottus ~]$ echo $GUS_CONFIG_FILE
>>>>>/home/sfischer/.gus.properties
>>>>>[sfischer@cottus ~]$ more $GUS_CONFIG_FILE
>>>>>databaseLogin=your_login
>>>>>databasePassword=your_password
>>>>>
>>>>>readOnlyDatabaseLogin=your_login
>>>>>readOnlyDatabasePassword=your_password
>>>>>
>>>>>dbiDsn=dbi:Oracle:host=cbilbld.pcbi.upenn.edu;sid=cbilbld #your
>>>>>dsn string here
>>>>>
>>>>>coreSchemaName=Core
>>>>>userName=sfischer #your user name here
>>>>>group=CBIL # your group name here
>>>>>project=GUS # your project here
>>>>>[sfischer@cottus ~]$
>>>>>
>>>>>
>>>>>
>>>>>marc jackson wrote:
>>>>>
>>>>>>Hello,
>>>>>> I"m having a problem getting GUS to install/compile. I"ve been
>>>>>>able to configure the database, but when I go to run the
>>>>"ga"
>>>>>>command to bootstrap in data. it pukes. In working with Ed
>>>>>>Robinson, we got to the 2nd build. Specifically:
>>>>>> build GUS install -append returns the following error:
>>>>>> [exec] Required property "group" must be specified in at
>>>>>>/opt/gus/gus_home/lib/perl/CBIL/Util/PropertySet.pm line 53.
>>>>>>BUILD FAILED
>>>>>>/opt/gus/project_home/install/build.xml:26: The following error
>>>>>>occurred while executing this line:
>>>>>>/opt/gus/project_home/GUS/build.xml:190: exec returned: -1
>>>>>> any help would be appreacited.
>>>>>> Regards,
>>>>>> Marc
>>
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