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RE: [Gusdev-gusdev] Problem building WDK on Fedora
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From: Dave B. <db...@pc...> - 2005-01-27 16:06:04
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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
>>>>>>>>>> >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
>>>>
>>>>
>
|
