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Re: [GUSDEV] dropping GUS schemas
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From: chawla <ch...@bi...> - 2011-05-02 11:19:09
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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...> 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...>
>>> Subject: Re: [GUSDEV] Build failed - couldn't install GUS
>>> To: Chris Stoeckert <sto...@pc...>
>>> Cc: gus...@li..., chawla <ch...@bi...>
>>> Message-ID: <BAN...@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...>
>>>
>>>
>>>>
>>>
>>
>>
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