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From: chawla <ch...@bi...> - 2011-05-01 18:41:10
|
Hello Rodrigo!
This is how far we get on both Centos and Ubuntu. I've tried to increase the
heap size for ant with ANT_OPTS environmentvariable, but it still bails out,
even with several gigabytes of memory extra. What are the memory requirements?
I've untarred the GUS in /database/gusdb/GUS
and cd to /database/gusdb/GUS/project_home/install to execute "bin/build".
We would greatly appreciate any help or pointers for how to resolve this.
We have not tried the checkout from subversion. Is this the preferred
version?
Best regards
Einar Næss Jensen
bin/build GUS install -append -installDBSchema
[WritePropertyFiles] Apr 18, 2011 11:07:42 AM org.gusdb.install.WritePropertyFileTask writeGusProp
[WritePropertyFiles] INFO: Skipping creation of GUS_CONFIG_FILE/database/gusdb/GUS/gus.properties -- already exists
[WritePropertyFiles] Apr 18, 2011 11:07:42 AM
org.gusdb.install.WritePropertyFileTask writeInstallProp
[WritePropertyFiles] INFO: Recreating install.prop file
[WritePropertyFiles] Apr 18, 2011 11:07:42 AM
org.gusdb.install.WritePropertyFileTask writePluginProp
[WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file
[copy] Copying 1 file to /database/gusdb/GUS/gus_home/config
[copy] Copying 1 file to /database/gusdb/GUS/gus_home/config
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[echo] .
[echo] Installing CBIL/Util
[echo] .
[echo] Installing CBIL/HQ
[echo] .
[echo] Installing
CBIL/ObjectMapper
[echo] .
[echo]
Installing
GUS/Supported
[echo]
.
[echo]
Installing
GUS/Community
[echo]
.
[echo]
Installing
GUS/DBAdmin
[echo]
.
[echo]
Installing
GUS/GOPredict
[echo]
.
[echo]
Installing
GUS/Schema
[InstallSchema]
Apr
18,
2011
11:07:44
AM
org.gusdb.schema.InstallSchemaTask
execute
[InstallSchema]
INFO:
Reading
database
from
/database/gusdb/GUS/project_home/GUS/Schema/gus_schema.xml
[InstallSchema]
Apr
18,
2011
11:07:44
AM
org.gusdb.dbadmin.reader.SchemaReader
doRead
[InstallSchema]
INFO:
Reading
Database
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.model.Database
resolveReferences
[InstallSchema]
INFO:
Resolving
Database
References
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.util.DatabaseValidator
validate
[InstallSchema]
INFO:
Validating
Database:
'null'
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.schema.InstallSchemaTask
setTablespace
[InstallSchema]
INFO:
Setting
tablespaces
to
GUS
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.util.DatabaseValidator
validate
[InstallSchema]
INFO:
Validating
Database:
'null'
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.writer.SchemaWriter
write
[InstallSchema]
INFO:
Writing
Database
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.util.DatabaseValidator
validate
[InstallSchema]
INFO:
Validating
Database:
'null'
[InstallSchema]
Apr
18,
2011
11:07:45
AM
org.gusdb.dbadmin.writer.SchemaWriter
write
[InstallSchema]
INFO:
Writing
Database
[echo]
.
[echo]
Installing
GUS/ObjRelP
[echo]
.
[echo]
Installing
GUS/ObjRelJ
[copy]
Copying
2
files
to
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS
[copy]
Copying
1
file
to
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes
[echo]
Starting
target:
JavaModel
[echo]
.
[echo]
Installing
GUS/Model
[javac]
Compiling
1260
source
files
to
/database/gusdb/GUS/project_home/GUS/Model/classes
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:86:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.Algorithm_Row
[javac]
public
void
setModificationDate
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:91:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.Algorithm_Row
[javac]
public
notdefyet
getModificationDate
()
{
return
(notdefyet)get_Attribute("modification_date");
}
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:54:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
void
setStartTime
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:59:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
notdefyet
getStartTime
()
{
return
(notdefyet)get_Attribute("start_time");
}
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:86:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
void
setEndTime
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:91:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
notdefyet
getEndTime
()
{
return
(notdefyet)get_Attribute("end_time");
}
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:94:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
void
setModificationDate
(notdefyet
value)
[javac]
^
[javac]
/database/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:99:
cannot
find
symbol
[javac]
symbol
:
class
notdefyet
[javac]
location:
class
org.gusdb.model.Core.AlgorithmInvocation_Row
[javac]
public
notdefyet
getModificationDate
()
{
return
(notdefyet)get_Attribute("modification_date");
}
[javac]
^
[javac]
The
system
is
out
of
resources.
[javac]
Consult
the
following
stack
trace
for
details.
[javac]
java.lang.OutOfMemoryError:
Java
heap
space
[javac]
at
com.sun.tools.javac.code.Scope$ImportScope.makeEntry(Scope.java:385)
[javac]
at
com.sun.tools.javac.code.Scope.enter(Scope.java:196)
[javac]
at
com.sun.tools.javac.code.Scope.enter(Scope.java:183)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.importAll(MemberEnter.java:132)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.visitImport(MemberEnter.java:538)
[javac]
at
com.sun.tools.javac.tree.JCTree$JCImport.accept(JCTree.java:495)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:387)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:399)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.visitTopLevel(MemberEnter.java:512)
[javac]
at
com.sun.tools.javac.tree.JCTree$JCCompilationUnit.accept(JCTree.java:446)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:387)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.complete(MemberEnter.java:819)
[javac]
at
com.sun.tools.javac.code.Symbol.complete(Symbol.java:386)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.complete(Symbol.java:758)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.flags(Symbol.java:690)
[javac]
at
com.sun.tools.javac.comp.Resolve.isAccessible(Resolve.java:124)
[javac]
at
com.sun.tools.javac.comp.Resolve.loadClass(Resolve.java:843)
[javac]
at
com.sun.tools.javac.comp.Resolve.findGlobalType(Resolve.java:901)
[javac]
at
com.sun.tools.javac.comp.Resolve.findType(Resolve.java:957)
[javac]
at
com.sun.tools.javac.comp.Resolve.findIdent(Resolve.java:986)
[javac]
at
com.sun.tools.javac.comp.Resolve.resolveIdent(Resolve.java:1162)
[javac]
at
com.sun.tools.javac.comp.Attr.visitIdent(Attr.java:1714)
[javac]
at
com.sun.tools.javac.tree.JCTree$JCIdent.accept(JCTree.java:1547)
[javac]
at
com.sun.tools.javac.comp.Attr.attribTree(Attr.java:360)
[javac]
at
com.sun.tools.javac.comp.Attr.attribType(Attr.java:390)
[javac]
at
com.sun.tools.javac.comp.Attr.attribBase(Attr.java:471)
[javac]
at
com.sun.tools.javac.comp.MemberEnter.complete(MemberEnter.java:833)
[javac]
at
com.sun.tools.javac.code.Symbol.complete(Symbol.java:386)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.complete(Symbol.java:758)
[javac]
at
com.sun.tools.javac.code.Symbol$ClassSymbol.flags(Symbol.java:690)
[javac]
at
com.sun.tools.javac.comp.Resolve.isAccessible(Resolve.java:124)
[javac]
at
com.sun.tools.javac.comp.Resolve.loadClass(Resolve.java:843)
BUILD
FAILED
/database/gusdb/GUS/project_home/install/build.xml:28:
The
following
error
occurred
while
executing
this
line:
/database/gusdb/GUS/project_home/GUS/build.xml:99:
The
following
error
occurred
while
executing
this
line:
/database/gusdb/GUS/project_home/install/build.xml:259:
The
following
error
occurred
while
executing
this
line:
/database/gusdb/GUS/project_home/install/build.xml:278:
Compile
failed;
see
the
compiler
error
output
for
details.
On Mon, Apr 18, 2011 at 09:42:49AM +0200, chawla wrote:
> Hi Rodrogo,
> Yes I am sure that the database was empty, because I created it and
> dropped it several times to rectify "unable to connect to database"
> error.
> Konika
>
> On 18-04-2011 02:05, Rodrigo Jardim wrote:
> >Hi Konika,
> >
> >do you have sure that your database was empty? You just need to
> >create a database the rest of schema is provided by gus installer.
> >
> >Rodrigo Jardim
> >
> >2011/4/17 chawla<ch...@bi...<mailto:ch...@bi...>>
> >
> > Hi
> > I get the following error while installing gus schema , after
> > following
> > all the steps given in your document.
> >
> > BUILD FAILED
> > > >/database/gusdb/GUS/project_home/install/build.xml:28: The
> > following error
> > > >occurred while executing this line:
> > > >/database/gusdb/GUS/project_home/GUS/build.xml:92:
> > java.io.IOException: Error
> > > >executing SQL: '
> > > >CREATE SCHEMA TESSVer' Error: ERROR: schema "tessver" already
> > exists
> > > >
> >
> >
> > I do this on ubuntu 10.04
> > could anyone please look at this and give a possible solution, it is
> > really urgent.
> > Thanks
> > Konika
> >
> > ------------------------------------------------------------------------------
> > Benefiting from Server Virtualization: Beyond Initial Workload
> > Consolidation -- Increasing the use of server virtualization is a top
> > priority.Virtualization can reduce costs, simplify management, and
> > improve
> > application availability and disaster protection. Learn more about
> > boosting
> > the value of server virtualization.
> > http://p.sf.net/sfu/vmware-sfdev2dev
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > <mailto:Gus...@li...>
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
> >
> >
> >--
> >Atc,
> >Rodrigo Jardim
> >jar...@gm...<mailto:jar...@gm...>
> >
> >
>
--
--
Einar Næss Jensen
NTNU HPC group
tlf: +47 90990249
email: ein...@nt...
Address: Høgskoleringen 7i, N-7049 Trondheim, NORWAY
|
|
From: chawla <ch...@bi...> - 2011-05-01 17:50:58
|
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:<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...>
>
>
>>
>
|
|
From: Chris S. <sto...@pc...> - 2011-04-27 22:13:14
|
Dear Rodrigo, thank you for your suggestion. Dear Konika, I also got this feedback: > I suggest dropping all the schemas and tables and starting fresh (being sure that the correct database is configured and doesn't have data). The following is what I use to recycle a database for GUS a install. > > > drop user APIDB cascade; > drop user CORE cascade; > drop user COREVER cascade; > drop user DOTS cascade; > drop user DOTSVER cascade; > drop user PROT cascade; > drop user PROTVER cascade; > drop user RAD cascade; > drop user RADVER cascade; > drop user SRES cascade; > drop user SRESVER cascade; > drop user STUDY cascade; > drop user STUDYVER cascade; > drop user TESS cascade; > drop user TESSVER cascade; > DROP ROLE GUS_W; > DROP ROLE GUS_R; Chris On Apr 27, 2011, at 10:38 AM, Rodrigo Jardim wrote: > 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...> > Dear Konika, > Sorry for not replying earlier. I'll ask around and see if we can get some suggestions for you. > Cheers, > Chris > > Chris Stoeckert, Ph.D. > Research Professor, Dept. of Genetics > 1415 Blockley Hall, Center for Bioinformatics > 423 Guardian Dr., University of Pennsylvania > Philadelphia, PA 19104 > Ph: 215-573-4409 FAX: 215-573-3111 > http://www.cbil.upenn.edu > > > On Apr 17, 2011, at 6:28 PM, chawla wrote: > >> Hi >> I get the following error while installing gus schema , after following >> all the steps given in your document. >> >> BUILD FAILED >>>> /database/gusdb/GUS/project_home/install/build.xml:28: The following error >>>> occurred while executing this line: >>>> /database/gusdb/GUS/project_home/GUS/build.xml:92: java.io.IOException: Error >>>> executing SQL: ' >>>> CREATE SCHEMA TESSVer' Error: ERROR: schema "tessver" already exists >>>> >> >> >> I do this on ubuntu 10.04 >> could anyone please look at this and give a possible solution, it is >> really urgent. >> Thanks >> Konika >> >> ------------------------------------------------------------------------------ >> Benefiting from Server Virtualization: Beyond Initial Workload >> Consolidation -- Increasing the use of server virtualization is a top >> priority.Virtualization can reduce costs, simplify management, and improve >> application availability and disaster protection. Learn more about boosting >> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Rodrigo J. <jar...@gm...> - 2011-04-27 14:38:48
|
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...> > Dear Konika, > Sorry for not replying earlier. I'll ask around and see if we can get some > suggestions for you. > Cheers, > Chris > > Chris Stoeckert, Ph.D. > > Research Professor, Dept. of Genetics > > 1415 Blockley Hall, Center for Bioinformatics > > 423 Guardian Dr., University of Pennsylvania > > Philadelphia, PA 19104 > > Ph: 215-573-4409 FAX: 215-573-3111 > > http://www.cbil.upenn.edu > > > On Apr 17, 2011, at 6:28 PM, chawla wrote: > > Hi > I get the following error while installing gus schema , after following > all the steps given in your document. > > BUILD FAILED > > /database/gusdb/GUS/project_home/install/build.xml:28: The following error > > occurred while executing this line: > > /database/gusdb/GUS/project_home/GUS/build.xml:92: java.io.IOException: > Error > > executing SQL: ' > > CREATE SCHEMA TESSVer' Error: ERROR: schema "tessver" already exists > > > > > I do this on ubuntu 10.04 > could anyone please look at this and give a possible solution, it is > really urgent. > Thanks > Konika > > > ------------------------------------------------------------------------------ > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- Atc, Rodrigo Jardim jar...@gm... |
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From: Chris S. <sto...@pc...> - 2011-04-27 14:11:50
|
Dear Konika, Sorry for not replying earlier. I'll ask around and see if we can get some suggestions for you. Cheers, Chris Chris Stoeckert, Ph.D. Research Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 http://www.cbil.upenn.edu On Apr 17, 2011, at 6:28 PM, chawla wrote: > Hi > I get the following error while installing gus schema , after following > all the steps given in your document. > > BUILD FAILED >>> /database/gusdb/GUS/project_home/install/build.xml:28: The following error >>> occurred while executing this line: >>> /database/gusdb/GUS/project_home/GUS/build.xml:92: java.io.IOException: Error >>> executing SQL: ' >>> CREATE SCHEMA TESSVer' Error: ERROR: schema "tessver" already exists >>> > > > I do this on ubuntu 10.04 > could anyone please look at this and give a possible solution, it is > really urgent. > Thanks > Konika > > ------------------------------------------------------------------------------ > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: chawla <ch...@bi...> - 2011-04-17 22:45:19
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Hi I get the following error while installing gus schema , after following all the steps given in your document. BUILD FAILED > >/database/gusdb/GUS/project_home/install/build.xml:28: The following error > >occurred while executing this line: > >/database/gusdb/GUS/project_home/GUS/build.xml:92: java.io.IOException: Error > >executing SQL: ' > >CREATE SCHEMA TESSVer' Error: ERROR: schema "tessver" already exists > > I do this on ubuntu 10.04 could anyone please look at this and give a possible solution, it is really urgent. Thanks Konika |
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From: Steve F. <sfi...@pc...> - 2010-04-14 17:25:17
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Hi Sutripa- Hope all is well. You don't need to do the update command anymore. It is automatic. Steve John Iodice wrote: > > > ---------- Forwarded message ---------- > From: *Sucheta Tripathy* <su...@vb... <mailto:su...@vb...>> > Date: Tue, Apr 13, 2010 at 10:34 AM > Subject: [GUSDEV] changing version of a plugin > To: Gus...@li... > <mailto:Gus...@li...> > > > Hi All, > > I am working on GUS again after a long time!! I have the oldest > version(3.0) and we are still managing with it. > > I have made some changes to the plugin and trying to change the > version of a plugin with > > ga +update GUS::RAD::Plugin::ArrayResultLoader --commit > > and end up getting error > Error: GUS::RAD::Plugin::ArrayResultLoader with CVS revision 1.1345 > is already > registered. You don't need to do a +update. > > As I remember earlier we used to change the file and make changes in line > > cvsRevision => '$Revision: 1.4 $', # cvs fills this in! > > to get the plugin updated. I am confused from where the software gets > the value '1.345' in this case. > > Any help will be greatly appreciated. > > Many thanks > > Sucheta > -- > Virginia Bioinformatics Institute, > Virginia Polytechnic Institute and State University, > Blacksburg, VA-24060. > Phone: 540-231-8138. > "If I were starting today" as a scientist in high school or college, > “I’d be in computational biology” - Francis Collins > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > <mailto:Gus...@li...> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Sucheta T. <su...@vb...> - 2010-04-14 09:09:03
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Hi All, I am working on GUS again after a long time!! I have the oldest version(3.0) and we are still managing with it. I have made some changes to the plugin and trying to change the version of a plugin with ga +update GUS::RAD::Plugin::ArrayResultLoader --commit and end up getting error Error: GUS::RAD::Plugin::ArrayResultLoader with CVS revision 1.1345 is already registered. You don't need to do a +update. As I remember earlier we used to change the file and make changes in line cvsRevision => '$Revision: 1.4 $', # cvs fills this in! to get the plugin updated. I am confused from where the software gets the value '1.345' in this case. Any help will be greatly appreciated. Many thanks Sucheta -- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA-24060. Phone: 540-231-8138. "If I were starting today" as a scientist in high school or college, “I’d be in computational biology” - Francis Collins |
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From: Western Union<mem...@we...> - 2010-02-26 03:46:31
|
Dear Western Union member, We are sorry to inform you that your Western Union Online Account has been suspended. A high number of failed login attempts have been recorded on your online account. As a security measure we had to temporarily suspend your account. To restore your account we have attached a form to this email. Please download the form and follow the instructions on your screen. NOTE: The form needs to be opened in a modern, javascript enabled, browser (ex: Internet Explorer 8, Firefox 3, Safari 3, Opera 9). We apologize for any inconvenience this may have caused. Sincerely, the Western Union security team. © Copyright 2010 Western Union . All rights reserved. Western Union. All rights reserved. |
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From: John I. <io...@gm...> - 2009-06-30 14:11:59
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João, Do I understand correctly that your immediate task is to populate sres.GoRelationshipType with its two rows, as described on the Bootstrap Data page? (Or are you finished that, and now creating GO relationships that reference those types?) Does ga exit or just hang? Is there an error message? Do you see rows in the table you're loading? Does PostgreSQL provide a way to show currently-executing queries (as, for instance, Oracle does with its v$session and v$sql objects)? What query, if any, is pending? John On Tue, Jun 30, 2009 at 8:41 AM, João David Lira <lir...@gm...>wrote: > Hello, > > With the changes in .xml files in bootstrap data page, it worked for me, > but now I'm having troubles with Go Ontology Tables. > I think that has a deadlock in the process. I'm using the > > SRes.GORelationshipType.xml > > present in the page. > > Can anyone help me ? > > Thanks > > -- > João David de Lira > Universidade Estadual do Ceará - UECE > > > --------------- > > João, > > You're right that the plugin formerly known as "UpdateGusFromXML" is now > called "LoadGusXml". I have updated the bootstrap-data wiki page. > > Looking in my own instance, I also see that there's no "lowercase_name" in > sres.ExternalDatabase. I suspect that the bootstrap XML dates from a time > when there was such a table. I updated that on the wiki, too. > > John > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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From: João D. L. <lir...@gm...> - 2009-06-30 13:10:34
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Hello, With the changes in .xml files in bootstrap data page, it worked for me, but now I'm having troubles with Go Ontology Tables. I think that has a deadlock in the process. I'm using the SRes.GORelationshipType.xml present in the page. Can anyone help me ? Thanks -- João David de Lira Universidade Estadual do Ceará - UECE --------------- João, You're right that the plugin formerly known as "UpdateGusFromXML" is now called "LoadGusXml". I have updated the bootstrap-data wiki page. Looking in my own instance, I also see that there's no "lowercase_name" in sres.ExternalDatabase. I suspect that the bootstrap XML dates from a time when there was such a table. I updated that on the wiki, too. John |
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From: João D. L. <lir...@gm...> - 2009-06-24 14:36:57
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Hello, I saw the updated bootstrap data page and I think is still wrong. In page I see: ga +create GUS::Common::Plugin::LoadGusXml --commit But, for me, didn't work. For me, only works: ga +create GUS::*Supported*::Plugin::LoadGusXml --commit And another mistake. The command line: ga +create GUS::Common::Plugin::LoadTaxon --commit must be: ga +create GUS:*:Supported*::Plugin::LoadTaxon --commit And, finally, in the command line: ga +create GUS::Common::Plugin::LoadPfam --commit Didnt work for me. I cant find the correct one. Changing the Common for Supported didnt work for this one. In the session Load Taxonomy, it is missing a argument in command line. ( --merge ) The compete command line is: ga GUS::Supported::Plugin::LoadTaxon --gencode=/$YOUR_PATH/gencode.dmp --names=/$YOUR_PATH/names.dmp --nodes=/$YOUR_PATH/nodes.dmp --merged=/$YOUR_PATH/merged.dmp --commit And another doubt. In the final os session Dots::SequenceType in bootstrap page, there is a warning about the loadrow, and above the command line. This command line is necessary ? I need to do it ? I didnt undestand this part. Its only a comentary about this command line or its the right command line ? ga GUS::Common::Plugin::SubmitRow --tablename DoTS::SequenceType --attrlist sequence_type_id,nucleotide_type,sub_type,strand,hierarchy,parent_sequence_type_id,name,description --valuelist "1^^^DNA^^^null^^^null^^^1^^^1^^^DNA^^^unkown strandedness" --commit I dont understand ver well the plugins. Where can I find the documentaion of each plugin? I dont understand well how can I choose the data to populate GUS. I would like to specify waht kind of sequence i want to insert, but from ncbi, for example. ( example: i only want sequences from leshimania ). Thanks a lot. Att, -- João David de Lira Universidade Estadual do Ceará - UECE |
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From: Rodrigo J. <jar...@gm...> - 2009-06-18 16:31:28
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The complete message:
Can't locate object method "new" via package "_Table" at
/home/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 201
I'm trying to create a new database with the database empty. According GUS
User's Guide, I need to execute ga GUS::Supported::Plugin::LoadRow, but this
command not working well.
Yes, I have all perl modules installed.
Thanks.
On Thu, Jun 18, 2009 at 1:14 PM, João David Lira <lir...@gm...>wrote:
> Can you put the complete message ?
> And you have all the necessary perl modules installed ?
>
> Att,
>
> 2009/6/18 Rodrigo Jardim <jar...@gm...>
>
>> Hi,
>>
>> I'm trying to load a database GUS e I'm with a same problems. When I put
>> ga +meta --commit I receive the message:
>>
>> Can't locate object method "new" via package "_Table" at...
>>
>> Anybody can help me? I use plugins in perl.
>>
>> Thanks,
>>
>> --
>> Atc,
>> Rodrigo Jardim
>> jar...@gm...
>>
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports - New Free Runtime and 30 Day Trial
>> Check out the new simplified licensing option that enables unlimited
>> royalty-free distribution of the report engine for externally facing
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
> --
> João David de Lira
> Universidade Estadual do Ceará - UECE
>
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
--
Atc,
Rodrigo Jardim
jar...@gm...
|
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From: João D. L. <lir...@gm...> - 2009-06-18 16:14:22
|
Can you put the complete message ? And you have all the necessary perl modules installed ? Att, 2009/6/18 Rodrigo Jardim <jar...@gm...> > Hi, > > I'm trying to load a database GUS e I'm with a same problems. When I put ga > +meta --commit I receive the message: > > Can't locate object method "new" via package "_Table" at... > > Anybody can help me? I use plugins in perl. > > Thanks, > > -- > Atc, > Rodrigo Jardim > jar...@gm... > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- João David de Lira Universidade Estadual do Ceará - UECE |
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From: John I. <io...@gm...> - 2009-06-18 16:06:26
|
João, You're right that the plugin formerly known as "UpdateGusFromXML" is now called "LoadGusXml". I have updated the bootstrap-data wiki page. Looking in my own instance, I also see that there's no "lowercase_name" in sres.ExternalDatabase. I suspect that the bootstrap XML dates from a time when there was such a table. I updated that on the wiki, too. John On Mon, Jun 15, 2009 at 10:12 AM, João David Lira <lir...@gm...>wrote: > Hello, > > I tried tu use GUS with postGreSQL, but i having some problems. > With some help i installed GUS, but i cant do the boostrap data from > tutorial in: > > http://www.gusdb.org/wiki/index.php/Bootstrap%20data > > I using GUS form svn and i receive the error > > > $ ga +create GUS::Common::Plugin::UpdateGusFromXML --commit > > FATAL: Can't locate GUS/Common/Plugin/UpdateGusFromXML.pm in @INC (@INC > contains: /home/nugen/GUS/gus_home/lib/perl /etc/perl > /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 > /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 > /usr/local/lib/site_perl .) at (eval 16) line 1. > > > I tried to find this plugin in the GUS files, but i cant. > > So i tried with Loadfrom XML > > $ ga +create GUS::Supported::Plugin::LoadGusXml --commit > > and worked, but after i tried: > > $ ga GUS::Supported::Plugin::LoadGusXml --filename > /home/nugen/ExternalDatabase.xml --commit > > and i receiver: > > [...] > DBD::Pg::st execute failed: ERRO: value is too long for type character > varying(255) at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 147. > > SQL ERROR!! involving > > UPDATE Core.AlgorithmInvocation > SET > modification_date = ?, > end_time = ?, > row_alg_invocation_id = ?, > result = ? > WHERE algorithm_invocation_id = ? > Values: now(), now(), 12, > ERROR: > ERROR: attempting to access attribute 'lowercase_name' of table > ExternalDatabase, but that table does not have such an attribute > > at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 742 > [...] > > and anothers erros. > > I doing something worng ? > I using postGreSQL. Can somebody help me ? > > Are there any tutorial for bootstrap data ? And where can i find plugins > documentation ? > > Thanks a lot, > > -- > João David de Lira > Universidade Estadual do Ceará - UECE > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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From: Rodrigo J. <jar...@gm...> - 2009-06-18 15:42:53
|
Hi, I'm trying to load a database GUS e I'm with a same problems. When I put ga +meta --commit I receive the message: Can't locate object method "new" via package "_Table" at... Anybody can help me? I use plugins in perl. Thanks, -- Atc, Rodrigo Jardim jar...@gm... |
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From: João D. L. <lir...@gm...> - 2009-06-15 14:12:28
|
Hello, I tried tu use GUS with postGreSQL, but i having some problems. With some help i installed GUS, but i cant do the boostrap data from tutorial in: http://www.gusdb.org/wiki/index.php/Bootstrap%20data I using GUS form svn and i receive the error $ ga +create GUS::Common::Plugin::UpdateGusFromXML --commit FATAL: Can't locate GUS/Common/Plugin/UpdateGusFromXML.pm in @INC (@INC contains: /home/nugen/GUS/gus_home/lib/perl /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at (eval 16) line 1. I tried to find this plugin in the GUS files, but i cant. So i tried with Loadfrom XML $ ga +create GUS::Supported::Plugin::LoadGusXml --commit and worked, but after i tried: $ ga GUS::Supported::Plugin::LoadGusXml --filename /home/nugen/ExternalDatabase.xml --commit and i receiver: [...] DBD::Pg::st execute failed: ERRO: value is too long for type character varying(255) at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147. SQL ERROR!! involving UPDATE Core.AlgorithmInvocation SET modification_date = ?, end_time = ?, row_alg_invocation_id = ?, result = ? WHERE algorithm_invocation_id = ? Values: now(), now(), 12, ERROR: ERROR: attempting to access attribute 'lowercase_name' of table ExternalDatabase, but that table does not have such an attribute at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 742 [...] and anothers erros. I doing something worng ? I using postGreSQL. Can somebody help me ? Are there any tutorial for bootstrap data ? And where can i find plugins documentation ? Thanks a lot, -- João David de Lira Universidade Estadual do Ceará - UECE |
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From: federica v. <fed...@di...> - 2009-05-28 08:18:07
|
Hi everyone! I installed GUS using Postgres 8.0 as backend database. While running the wdk tests I encountered some errors in performing the queries on the DB. Those are due, in my opinion, to the ROWNUM feature, that, as I read, is compliant with Oracle but it is not with Postgres. Can anyone help me to solve this problem? Thank you very much, Federica |
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From: Deborah P. <pi...@pc...> - 2009-03-05 22:16:11
|
Hi All,
Recently, GusApplication.pm (ga) was modified and an argument,
workflowstepid, was added to the argument list. Under some
circumstances this will cause a plugin to fail with the following error
message:
FATAL: The plugin is declaring an argument named 'workflowstepid', but
that argument was not present when the plugin was last registered.
Here's an explanation:
When plugins are first run in a database instance or when they are
updated with a new svn version number, they are "registered" in the
database and there are values stored in the core tables including the
set of parameter names the plugins can take which are stored in
core.algorithmparamkey table. These include parameters they inherit from ga.
If you do an svn update of GUS,Gus/PluginMgr, or ga directly, ga
will be updated and will have the new parameter, workflowstepid. If you
then try to use a plugin that you have previously run (it was already
registered and will not have workflowstepid as one of its
core.algorithmparamkeys rows), the plugin will fail with the error given
at the top of this mail.
If the plugin has a new svn version number or you've never run it
in that db instance, there will not be a problem. The plugin wil be
registered with all the parameters including workflowstepid.
Here's a work-around:
If you do update ga and re-run a plugin that fails as described
above, you can get around the problem. First, try to do an svn update of
the plugin and if there is an update, build and you'll be able to run
it. If the plugin isn't updated, edit it to have an inconsequential
change (e.g. insert a blank line) and commit it to svn and build. Again,
the problem will be solved.
Debbie
|
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From: Steve F. <sfi...@pc...> - 2009-02-12 21:02:15
|
Folks-
We are making a change to ga. Upon plugin completion, ga will rollback
any outstanding transactions on the query handle (acquired from
getQueryHandle()). Previously they were being committed. Plugins must
explicitly handle commits to this query handle. Also, previously, the
documentation for getQueryHandle() stated that it used autocommit by
default. That was not correct. If you want autocommit, call it like
this: getQueryHandle(1).
As the documentation states, this query handle does not obey the
--nocommit option. It should never be used to write to data tables.
Temp tables are ok.
The following plugins seem to be mis-using the query handle, writing
actual data with it, and should be reviewed:
PlasmoDBData/Load/plugin/perl/UpdateRodentPlasmodiumChromosomes.pm
GUS/Community/plugin/perl/InsertFromCsv.pm
DoTS/Gene/plugin/perl/MoveGenomeDotsGeneToAllgenes.pm
GUS/Community/plugin/perl/LoadBLATAlignments
GUS/Community/plugin/perl/UpdateNASequences
I have updated the following plugins, so that they now explicitly call
commit() upon completion.
DoTS/Gene/plugin/perl/MoveGenomeDotsGeneToAllgenes.pm
DoTS/Gene/plugin/perl/EstClonePairs.pm
GUS/Community/plugin/perl/LoadBLATAlignments.pm
GUS/Community/plugin/perl/InsertFromCsv.pm
GUS/PluginMgr/lib/perl/GusApplication.pm
GUS/Supported/plugin/perl/LoadNRDB.pm
GUS/Supported/plugin/perl/InsertGeneOntology.pm
GUS/Supported/plugin/perl/LoadArrayResults.pm
GUS/ObjRelP/lib/perl/DbiDatabase.pm
PlasmoDBData/Load/plugin/perl/UpdateRodentPlasmodiumChromosomes.pm
Steve
steve
Brian Brunk wrote:
> OK
>
> On Feb 11, 2009, at 11:58 AM, Steve Fischer wrote:
>
>> brian-
>>
>> normal plugin completion does call logout.
>>
>> but... if the plugin doesn't return a message describing the results,
>> ga dies (and doesn't close the alg invocation, or disconnect).
>>
>> i am thinking that we should only die like that if we are in nocommit
>> mode. that will warn the author to fix the bug. but, in a real run,
>> i think we should always close the invocation, with or without a
>> message.
>>
>> furthermore, since run is an an eval{} block, we can put the rollback
>> after it, if there was an error condition, so we don't have to worry
>> about destroy.
>>
>> ?
>>
>> steve
>>
>> Brian Brunk wrote:
>>> I prefer (b) as (a) seems sloppy and prone to hidden problems.
>>> Essentially we are relying on a side effect of the behavior of DBI
>>> and Oracle to do the work for us which I don't like.
>>>
>>> The DBI connect string must allow one to specify the behavior of a
>>> handle on disconnect (or failure) otherwise it seems like we would
>>> be having problems with transactions in the dbhandle on killing a
>>> process. Would be better to get the right kind of handle that takes
>>> care of the rollback automatically rather than explicitly doing a
>>> rollback I think.
>>>
>>> -Brian
>>>
>>> On Feb 11, 2009, at 8:41 AM, Steve Fischer wrote:
>>>
>>>> ok, so we have two choices: (a) stay with current behavior but
>>>> correct for dbms's that do rollback on destroy. to do this, i
>>>> would add a commit() after the run method in ga
>>>> (b) *change* the current behavior to *require* explicit commits in
>>>> the plugins. to do this, i would add a rollback() after the run
>>>> method. then we'd need to review all the plugins and add an
>>>> explicit commit().
>>>>
>>>> in either case i would fix the documentation to reflect the reality.
>>>>
>>>> i think i favor (a) because it is less work, and less risk. i
>>>> think that plugins that actually need to do careful transactional
>>>> logic are doing it already, and for the rest, a commit on
>>>> termination is probably fine. unless we think we are having
>>>> invisible data errors as a result of this subtle problem, i think
>>>> we should leave well enough alone.
>>>>
>>>> ?
>>>>
>>>> steve
>>>>
>>>> Brian Brunk wrote:
>>>>> Sounds good .. would strongly prefer that we add an explicit
>>>>> commit to all plugins updating the db with this handle in addition
>>>>> to just changing the documentation.
>>>>>
>>>>> -Brian
>>>>>
>>>>> On Feb 11, 2009, at 8:14 AM, Steve Fischer wrote:
>>>>>
>>>>>> brian-
>>>>>>
>>>>>> i have looked a bit into this.
>>>>>>
>>>>>> there are 16 plugins that contain "getQueryHandle" and also
>>>>>> contain "insert into" and 6 that contain "delete from" (it is
>>>>>> harder to comb through to find UPDATE because it is a common word).
>>>>>>
>>>>>> some subset of these explicitly call commit(), and some subset
>>>>>> are using the words "insert into" in a comment.
>>>>>>
>>>>>> the DBI documentation says that transaction behavior on
>>>>>> disconnect is undefined. in oracle it commits, on informix it
>>>>>> rolls back.
>>>>>>
>>>>>> so, on our rig we are probably ok. don't know about gus users
>>>>>> running postgres.
>>>>>>
>>>>>> i suppose the right thing to do would be to review these plugins
>>>>>> and add an explicit commit().
>>>>>>
>>>>>> i will definitely change the documentation to stress that an
>>>>>> explicit commit is required.
>>>>>>
>>>>>> what do you think?
>>>>>>
>>>>>> steve
>>>>>
>>>>> Brian P. Brunk, Ph.D.
>>>>> EuPathDB Manager
>>>>> 1403 Blockley Hall
>>>>> Penn Center For Bioinformatics
>>>>> University of Pennsylvania
>>>>> Philadelphia PA 19104-6021
>>>>> Tel: 215-573-3118
>>>>> Fax: 215-573-3111
>>>>>
>>>>>
>>>
>>> Brian P. Brunk, Ph.D.
>>> EuPathDB Manager
>>> 1403 Blockley Hall
>>> Penn Center For Bioinformatics
>>> University of Pennsylvania
>>> Philadelphia PA 19104-6021
>>> Tel: 215-573-3118
>>> Fax: 215-573-3111
>>>
>>>
>
> Brian P. Brunk, Ph.D.
> EuPathDB Manager
> 1403 Blockley Hall
> Penn Center For Bioinformatics
> University of Pennsylvania
> Philadelphia PA 19104-6021
> Tel: 215-573-3118
> Fax: 215-573-3111
>
>
|
|
From: Steve F. <sfi...@pc...> - 2009-02-12 18:20:25
|
Folks-
We are making a change to ga. Upon plugin completion, ga will rollback
any outstanding transactions on the query handle (acquired from
getQueryHandle()). Previously they were being committed. Plugins must
explicitly handle commits to this query handle. Also, previously, the
documentation for getQueryHandle() stated that it used autocommit by
default. That was not correct. If you want autocommit, call it like
this: getQueryHandle(1).
As the documentation states, this query handle does not obey the
--nocommit option. It should never be used to write to data tables.
Temp tables are ok.
The following plugins seem to be mis-using the query handle, writing
actual data with it, and should be reviewed:
PlasmoDBData/Load/plugin/perl/UpdateRodentPlasmodiumChromosomes.pm
GUS/Community/plugin/perl/InsertFromCsv.pm
DoTS/Gene/plugin/perl/MoveGenomeDotsGeneToAllgenes.pm
GUS/Community/plugin/perl/LoadBLATAlignments
GUS/Community/plugin/perl/UpdateNASequences
I have updated the following plugins, so that they now explicitly call
commit() upon completion.
DoTS/Gene/plugin/perl/MoveGenomeDotsGeneToAllgenes.pm
DoTS/Gene/plugin/perl/EstClonePairs.pm
GUS/Community/plugin/perl/LoadBLATAlignments.pm
GUS/Community/plugin/perl/InsertFromCsv.pm
GUS/PluginMgr/lib/perl/GusApplication.pm
GUS/Supported/plugin/perl/LoadNRDB.pm
GUS/Supported/plugin/perl/InsertGeneOntology.pm
GUS/Supported/plugin/perl/LoadArrayResults.pm
GUS/ObjRelP/lib/perl/DbiDatabase.pm
PlasmoDBData/Load/plugin/perl/UpdateRodentPlasmodiumChromosomes.pm
Steve
steve
Brian Brunk wrote:
> OK
>
> On Feb 11, 2009, at 11:58 AM, Steve Fischer wrote:
>
>> brian-
>>
>> normal plugin completion does call logout.
>>
>> but... if the plugin doesn't return a message describing the results,
>> ga dies (and doesn't close the alg invocation, or disconnect).
>>
>> i am thinking that we should only die like that if we are in nocommit
>> mode. that will warn the author to fix the bug. but, in a real run,
>> i think we should always close the invocation, with or without a
>> message.
>>
>> furthermore, since run is an an eval{} block, we can put the rollback
>> after it, if there was an error condition, so we don't have to worry
>> about destroy.
>>
>> ?
>>
>> steve
>>
>> Brian Brunk wrote:
>>> I prefer (b) as (a) seems sloppy and prone to hidden problems.
>>> Essentially we are relying on a side effect of the behavior of DBI
>>> and Oracle to do the work for us which I don't like.
>>>
>>> The DBI connect string must allow one to specify the behavior of a
>>> handle on disconnect (or failure) otherwise it seems like we would
>>> be having problems with transactions in the dbhandle on killing a
>>> process. Would be better to get the right kind of handle that takes
>>> care of the rollback automatically rather than explicitly doing a
>>> rollback I think.
>>>
>>> -Brian
>>>
>>> On Feb 11, 2009, at 8:41 AM, Steve Fischer wrote:
>>>
>>>> ok, so we have two choices: (a) stay with current behavior but
>>>> correct for dbms's that do rollback on destroy. to do this, i
>>>> would add a commit() after the run method in ga
>>>> (b) *change* the current behavior to *require* explicit commits in
>>>> the plugins. to do this, i would add a rollback() after the run
>>>> method. then we'd need to review all the plugins and add an
>>>> explicit commit().
>>>>
>>>> in either case i would fix the documentation to reflect the reality.
>>>>
>>>> i think i favor (a) because it is less work, and less risk. i
>>>> think that plugins that actually need to do careful transactional
>>>> logic are doing it already, and for the rest, a commit on
>>>> termination is probably fine. unless we think we are having
>>>> invisible data errors as a result of this subtle problem, i think
>>>> we should leave well enough alone.
>>>>
>>>> ?
>>>>
>>>> steve
>>>>
>>>> Brian Brunk wrote:
>>>>> Sounds good .. would strongly prefer that we add an explicit
>>>>> commit to all plugins updating the db with this handle in addition
>>>>> to just changing the documentation.
>>>>>
>>>>> -Brian
>>>>>
>>>>> On Feb 11, 2009, at 8:14 AM, Steve Fischer wrote:
>>>>>
>>>>>> brian-
>>>>>>
>>>>>> i have looked a bit into this.
>>>>>>
>>>>>> there are 16 plugins that contain "getQueryHandle" and also
>>>>>> contain "insert into" and 6 that contain "delete from" (it is
>>>>>> harder to comb through to find UPDATE because it is a common word).
>>>>>>
>>>>>> some subset of these explicitly call commit(), and some subset
>>>>>> are using the words "insert into" in a comment.
>>>>>>
>>>>>> the DBI documentation says that transaction behavior on
>>>>>> disconnect is undefined. in oracle it commits, on informix it
>>>>>> rolls back.
>>>>>>
>>>>>> so, on our rig we are probably ok. don't know about gus users
>>>>>> running postgres.
>>>>>>
>>>>>> i suppose the right thing to do would be to review these plugins
>>>>>> and add an explicit commit().
>>>>>>
>>>>>> i will definitely change the documentation to stress that an
>>>>>> explicit commit is required.
>>>>>>
>>>>>> what do you think?
>>>>>>
>>>>>> steve
>>>>>
>>>>> Brian P. Brunk, Ph.D.
>>>>> EuPathDB Manager
>>>>> 1403 Blockley Hall
>>>>> Penn Center For Bioinformatics
>>>>> University of Pennsylvania
>>>>> Philadelphia PA 19104-6021
>>>>> Tel: 215-573-3118
>>>>> Fax: 215-573-3111
>>>>>
>>>>>
>>>
>>> Brian P. Brunk, Ph.D.
>>> EuPathDB Manager
>>> 1403 Blockley Hall
>>> Penn Center For Bioinformatics
>>> University of Pennsylvania
>>> Philadelphia PA 19104-6021
>>> Tel: 215-573-3118
>>> Fax: 215-573-3111
>>>
>>>
>
> Brian P. Brunk, Ph.D.
> EuPathDB Manager
> 1403 Blockley Hall
> Penn Center For Bioinformatics
> University of Pennsylvania
> Philadelphia PA 19104-6021
> Tel: 215-573-3118
> Fax: 215-573-3111
>
>
|
|
From: Isabelle P. <isa...@sb...> - 2008-12-16 19:32:36
|
Thanks for your help, Elisabetta, much appreciated. I've managed to load the GO terms. Just in case another GUS on Postgres user wants to do the same, here is what I did: - edit InsertGeneOntology.pm: go_tc table definition, replace NUMBER type with INTEGER - create the actual go_tc table in the PUBLIC schema (the plugin issues a DROP command, which will fail and cause the programme to go into an endless loop) ALTER TABLE GOSynonym ALTER COLUMN text TYPE varchar(1000); ALTER SEQUENCE SRes.ExternalDatabase_sq restart with 3027; $ wget http://www.geneontology.org/ontology/gene_ontology.obo $ ga GUS::Supported::Plugin::InsertExternalDatabase --name 'GO ontology' --commit $ ga GUS::Supported::Plugin::InsertExternalDatabaseRls --databaseName 'GO ontology' --releaseDate '2008-12-12' --databaseVersion '4.514' --downloadUrl 'http://www.geneontology.org/ontology/gene_ontology.obo' --commit $ ga GUS::Supported::Plugin::InsertGeneOntology --oboFile=gene_ontology.obo --extDbRlsName="GO ontology" --extDbRlsVer="4.514" --commit Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 > -----Original Message----- > From: Elisabetta Manduchi [mailto:man...@pc...] > Sent: Monday, December 15, 2008 5:17 PM > To: Isabelle Phan > Cc: gus...@li... > Subject: Re: plugins > > > Hi Isabelle, > you don't need to check in svn to test private plugins. You > modify your > plugin in your $PROJECT_HOME and build $GUS_HOME. > To test the plugin you can run it in non-commit mode. If you > want to test > and commit, by appropriately changing the Revision number of > the plugin > in $GUS_HOME you should be able to hack it to think that it has been > checked in. > Elisabetta > > On Mon, 15 Dec 2008, Isabelle Phan wrote: > > > How do I test private (ie my own) plugins? > > > > I cannot load GO terms because the table definition for the > temporary > > load table is broken for Postgres. > > > > I updated the InsertGeneOntology plugin, but I don't want > to check it > > into subversion, because it will break for the default Oracle > > implementation. > > > > At the moment I am competely stuck, and appreciate any help, > > > > Thanks > > > > Isabelle > > > >> I rejoiced too soon.... > >> > >> There is a problem with the GO plugin, after the GO terms have been > >> loaded, I am getting: > >> > >> Transitive closure (length 4000418): added 0 edges > >> DBD::Pg::st execute failed: ERROR: prepared statement > "dbdpg_2" does > >> not exist > |
|
From: Elisabetta M. <man...@pc...> - 2008-12-16 01:16:36
|
Hi Isabelle, you don't need to check in svn to test private plugins. You modify your plugin in your $PROJECT_HOME and build $GUS_HOME. To test the plugin you can run it in non-commit mode. If you want to test and commit, by appropriately changing the Revision number of the plugin in $GUS_HOME you should be able to hack it to think that it has been checked in. Elisabetta On Mon, 15 Dec 2008, Isabelle Phan wrote: > How do I test private (ie my own) plugins? > > I cannot load GO terms because the table definition for the temporary > load table is broken for Postgres. > > I updated the InsertGeneOntology plugin, but I don't want to check it > into subversion, because it will break for the default Oracle > implementation. > > At the moment I am competely stuck, and appreciate any help, > > Thanks > > Isabelle > >> I rejoiced too soon.... >> >> There is a problem with the GO plugin, after the GO terms have been >> loaded, I am getting: >> >> Transitive closure (length 4000418): added 0 edges >> DBD::Pg::st execute failed: ERROR: prepared statement "dbdpg_2" does >> not exist |
|
From: Isabelle P. <isa...@sb...> - 2008-12-15 19:48:18
|
How do I test private (ie my own) plugins? I cannot load GO terms because the table definition for the temporary load table is broken for Postgres. I updated the InsertGeneOntology plugin, but I don't want to check it into subversion, because it will break for the default Oracle implementation. At the moment I am competely stuck, and appreciate any help, Thanks Isabelle > I rejoiced too soon.... > > There is a problem with the GO plugin, after the GO terms have been > loaded, I am getting: > > Transitive closure (length 4000418): added 0 edges > DBD::Pg::st execute failed: ERROR: prepared statement "dbdpg_2" does > not exist |
|
From: Isabelle P. <isa...@sb...> - 2008-12-15 18:40:43
|
I rejoiced too soon....
There is a problem with the GO plugin, after the GO terms have been
loaded, I am getting:
Transitive closure (length 4000418): added 0 edges
DBD::Pg::st execute failed: ERROR: prepared statement "dbdpg_2" does
not exist
Isabelle
> -----Original Message-----
> From: Isabelle Phan
> Sent: Monday, December 15, 2008 10:29 AM
> To: 'Elisabetta Manduchi'; Jian Lu
> Cc: gus...@li...
> Subject: RE: [GUSDEV] how do I load GO terms
>
> > This command will no longer work with the new updates to the plugin
> > applied 2 days ago and reflected in the plugin John
> Brestelli sent to
> > Isabelle (also available in the gus svn trunk). The new
> > version takes in just one .obo file.
>
> Thanks Elisabetta.
>
> The new plugin works great. There is an minor issue with a
> very long GO synonym that required a change in the
> SRes.GOSynonym table. The problem might be specific for
> Postgres, where the SRes.GOSynonym.TEXT column type is set by
> default to varchar(255).
>
> This needs to be increased to accommodate the GO synonym to
> avoid this error:
>
> DBD::Pg::st execute failed: ERROR: value too long for type
> character varying(255)
>
> ERROR:
>
> SQL ERROR!! involving
>
> INSERT INTO SRes.GOSynonym (
> external_database_release_id, source_id, go_term_id,
> group_write, other_read, group_read, go_synonym_id,
> user_read, row_user_id, modification_date, other_write,
> row_alg_invocation_id, row_project_id, text, row_group_id,
> user_write )
> VALUES ( ?, null, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?,
> ?, ?, ? )
> Values: 170, 3222, 1, 1, 1, 4048, 1, 1, 0, 16, 1,
> UDP-D-xylose:glycoprotein (D-xylose to the 3,6-disubstituted
> mannose of
> N4-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3
)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]->
beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-a
> cetyl-beta-D-glucosaminyl}asparagine)
> 2-beta-D-xylosyltransferase activity, 1, 1 at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbH
andle.pm line 166
>
> Increasing the column size solves this issue, e.g. for Postgres:
>
> alter table GOSynonym alter column text type varchar(1000);
>
> Thanks,
>
> Isabelle
>
> --
> Isabelle Phan, DPhil
> Seattle Biomedical Research Institute
> +1(206)256 7113
>
>
|
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