From: Dave B. <db...@pc...> - 2005-01-25 16:05:55
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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 You probably took that command from our wdk wiki documentation; apparently the command is out of date and will be changed.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 >>> >>> > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! 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