[GUSDEV] installing GUS on postgresql

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This error:

*[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to
locate class*
[InstallSchema] java.lang.
ClassNotFoundException: oracle.jdbc.OracleDriver

seems like the result of acting like an Oracle install in a postgres
environment. Is there a file under $GUS_HOME that says "oracle" where it
should say "postgresql"?

-- John

On Mon, May 2, 2011 at 7:18 AM, chawla <ch...@bi...> wrote:

>  Hi
> I was using the one available on website that is GUS-3.5.0.0.tar.gz and it
> didn't had the mentioned code lines in GeneratorFunction.pm,
> so now I downloaded the current verion from the subversion directory as
> mentioned on webiste.
> it is slightly different from the previous version in the sense it required
> "gus.config" file to be present at "/home/chawla/GUS/gus_home/config"
> I remade the user and database in postgres , and copied the old gus.config
> at "/home/chawla/GUS/gus_home/config"
> and now the errors are different:
>
> Buildfile: /home/chawla/GUS/project_home/install/build.xml
>
> install:
>      [echo]  proj=GUS
>      [echo]  comp=
>
> defaultComponentInstall:
>      [echo] .
>      [echo] Installing CBIL/Bio
>
> recordBuildState:
> [propertyfile] Updating property file: /home/chawla/GUS/gus_home/config/.
> build.info
>
> defaultComponentInstall:
>      [echo] .
>      [echo] Installing CBIL/CSP
>
> recordBuildState:
> [propertyfile] Updating property file: /home/chawla/GUS/gus_home/config/.
> build.info
>
> defaultComponentInstall:
>      [echo] .
>      [echo] Installing CBIL/Util
> ................similar lines............................
>
> InstallSchema:
> *[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to
> locate class*
> [InstallSchema] java.lang.ClassNotFoundException: oracle.jdbc.OracleDriver
> [InstallSchema]     at
> org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader.java:1400)
> [InstallSchema]     at
> org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1341)
>
> ................similar lines....................
>
> BUILD FAILED
> /home/chawla/GUS/project_home/install/build.xml:37: The following error
> occurred while executing this line:
> /home/chawla/GUS/project_home/GUS/build.xml:16: The following error
> occurred while executing this line:
> /home/chawla/GUS/project_home/GusSchema/build.xml:62: Unable to locate
> class
>
> I checked build.xml line 62
> schema="${projectsDir}/GusSchema/Definition/config/gus_schema.xml"/>
> which seems to be present at the correct place.
>
> Hope you can help
> Konika
>
>
>
> On 05/02/2011 03:50 AM, Mark Heiges wrote:
>
> Hi Konika,
>
> Sorry, we assumed you were using Oracle when we sent the 'drop user'
> instructions. John is right about the syntax for postgres. Also, the
> instruction to drop the ApiDB schema was included by mistake in the earlier
> email. That schema is custom for our project so doesn't apply to you.
>
> What version of GUS are you using? The notdefyet error may be the result of
> an old bug that was fixed in 2005. The GUS-3.5.0.0.tar.gz file on the
> download site does not have the fix.
>
> Check the file GUS/ObjRelP/lib/perl/Generator/GeneratorFunctions.pm to see
> if it has this elsif statement around line 48:
>
>    elsif (uc($oraType) eq "TIMESTAMP" ) {
>        $newType .= "Timestamp";
>    }
>
> I'm attaching a patched version GeneratorFunctions.pm.
>
> Alternatively you can checkout the most recent code from the Subversion
> repository. I have successfully installed the GUS schema in Postgres with
> that code.
> See http://www.gusdb.org/download.php .
>
> Mark Heiges
> EuPathDB Bioinformatics Resource Center
> Center for Tropical and Emerging Global Diseases
> Paul D. Coverdell Center, Rm 370
> 500 D. W. Brooks Drive
> University of Georgia, Athens, GA 30602
>
>
> On May 1, 2011, at 6:53 PM, John Iodice wrote:
>
> "drop user apidb cascade" is the Oracle syntax. I think the equivalent for
> postgres is:
>
> drop schema apidb;
>
> -- John
>
> On Sun, May 1, 2011 at 1:50 PM, chawla <ch...@bi...><ch...@bi...>wrote:
> Hi all
> I tried dropping the database and user , with what suggested by Dr Chris.
> I was confused with the names used here such as  APIDB which doesn't looks
> looks like a user and thus I got the errors with these as shown below.
> but the database mygus and user gus_w was dropped successfully.
>
> After this I try to install gus again and got errors related to java. These
> are shown further below. Kindly suggest a possible solution.
>
>
> drop database mygus;
> DROP DATABASE
> postgres=# drop user APIDB cascade;
> ERROR:  syntax error at or near "cascade"
> LINE 1: drop user APIDB cascade;
>
>                         ^
> postgres=#  drop user STUDYVER cascade;
> ERROR:  syntax error at or near "cascade"
> LINE 1: drop user STUDYVER cascade;
>                            ^
> postgres=#  drop user TESS cascade;
> ERROR:  syntax error at or near "cascade"
> LINE 1: drop user TESS cascade;
>                        ^
> postgres=#  drop user TESSVER cascade;
> ERROR:  syntax error at or near "cascade"
> LINE 1: drop user TESSVER cascade;
>                           ^
> postgres=#  DROP ROLE gus_w;
> DROP ROLE
> postgres=#  DROP ROLE gus_r;
> **********************************************
> build GUS install -append -installDBSchema
>
> errors:
>  [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.SRes.ECPathway_Row
>     [javac]     public void setModificationDate (notdefyet value)
>     [javac]                                      ^
>     [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/ECPathway_Row.java:83:
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.SRes.ECPathway_Row
>     [javac]     public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
>     [javac]            ^
>     [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:78:
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
>     [javac]     public void setModificationDate (notdefyet value)
>     [javac]                                      ^
>     [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:83:
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
>     [javac]     public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
>     [javac]            ^
>     [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:86:
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
>     [javac]     public void setModificationDate (notdefyet value)
>     [javac]                                      ^
>     [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:91:
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
>     [javac]     public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
>     [javac]            ^
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 100 errors
>
> Thanks
> Konika
>
>
> On 04/28/2011 12:13 AM, gus...@li... wrote:
>
>
>
>
> ------
>
> Message: 3
> Date: Wed, 27 Apr 2011 11:38:40 -0300
> From: Rodrigo Jardim <jar...@gm...> <jar...@gm...>
> Subject: Re: [GUSDEV] Build failed - couldn't install GUS
> To: Chris Stoeckert <sto...@pc...> <sto...@pc...>
> Cc: gus...@li..., chawla <ch...@bi...><ch...@bi...>
> Message-ID: <BANLkTi=KeiJwV=d9i...@ma...><BANLkTi=KeiJwV=d9i...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Konika,
>
> I think your problem could be solved with the parameters -Xmx and -Xms in
> java (JRE). But, I don't know where you put this in the scripts of GUS.
> Maybe Dr. Chris know.  I hope I have helped you. (sorry for my english!)
>
> Regards,
> Rodrigo Jardim
>
> 2011/4/27 Chris Stoeckert <sto...@pc...><sto...@pc...>
>
>
>
>
>
>
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