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From: Michael S. <msa...@pc...> - 2005-12-08 18:16:13
|
Hi Ricardo, GUS doesn't have direct support for workflows or webservices. There are, however, several groups that are using GUS as the data storage system for web services. This usually involves writing a small amount of code to extract the data and deliver it. There are also some groups that have expressed an interest in using GUS with workflows, so this is a good area for collaboration and development. GUS does have a pipeline API, but I suspect it's not quite what you're looking for. --Mike On Dec 8, 2005, at 1:09 PM, Ricardo Balbi wrote: > Hi, > > A doubt: > Has support for management of workflows in some schema of > gus ? Support for storage of the definition, instances, in and out > parameters, etc. > Also has support for web services? > > []'s, > Ricardo Balbi |
|
From: Ricardo B. <rb...@gm...> - 2005-12-08 18:10:06
|
Hi,
A doubt:
Has support for management of workflows in some schema of gus ? Suppor=
t
for storage of the definition, instances, in and out parameters, etc.
Also has support for web services?
[]'s,
Ricardo Balbi
|
|
From: Michael S. <msa...@pc...> - 2005-12-08 13:46:24
|
All, We are preparing for the next release of GUS, which will consist of GusSchema 3.6 and the Application Framework 2.1. The hope and intent is that this release will be available before the holidays. As with previous releases, we're using the tracker to identify and address issues that should be included in the release. The tracker is available at: https://www.cbil.upenn.edu/tracker/ If you have a request for a feature or a bug that should be addressed in the next release, please make sure that it has been submitted to the tracker by 12/12. The goal will then be to have GUS enter QA by 12/16 with a release on or around 12/23. The next release of GUS will formalize all of the recent changes that are present in the source repository trunk. This includes the InsertSequenceFeatures plugin, fixes and enhancements to the installer, bug fixes and additions (including schema changes). SQL upgrade scripts from 3.5.1 will be provided (and scripts exist from 3.5 to 3.5.1) Please post to the list if you have any questions/comments/ suggestions or if you'd like to help contribute but aren't sure about how to get involved! Thanks, Mike and GUS Community |
|
From: Ricardo B. <rb...@gm...> - 2005-12-08 11:04:36
|
Thanks Mark,
But now I have another error.
It follows below:
[rbalbi1@crithidia bancos]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
$GUS_HOME/config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt
--fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer
"2005-12-06" --commit
Thu Dec 8 09:04:53 2005 ARG algoinvo 1
Thu Dec 8 09:04:53 2005 ARG comment
Thu Dec 8 09:04:53 2005 ARG commit 1
Thu Dec 8 09:04:53 2005 ARG debug 0
Thu Dec 8 09:04:53 2005 ARG defaultOrganism
Thu Dec 8 09:04:53 2005 ARG extDbName Kinetoplastida_nt
Thu Dec 8 09:04:53 2005 ARG extDbRlsVer 2005-12-06
Thu Dec 8 09:04:53 2005 ARG fileFormat genbank
Thu Dec 8 09:04:53 2005 ARG gff2GroupTag
Thu Dec 8 09:04:53 2005 ARG group
Thu Dec 8 09:04:53 2005 ARG gusconfigfile
/GUS/gus_home/config/gus.config
Thu Dec 8 09:04:53 2005 ARG handlerExternalDbs
Thu Dec 8 09:04:53 2005 ARG help
Thu Dec 8 09:04:53 2005 ARG helpHTML
Thu Dec 8 09:04:53 2005 ARG inputFileExtension
Thu Dec 8 09:04:53 2005 ARG inputFileOrDir kinetoplastida_nt
Thu Dec 8 09:04:53 2005 ARG makeSourceids
Thu Dec 8 09:04:53 2005 ARG mapFile
/GUS/gus_home/config/genbank2gus.xml
Thu Dec 8 09:04:53 2005 ARG naSequenceSubclass
Thu Dec 8 09:04:53 2005 ARG project
Thu Dec 8 09:04:53 2005 ARG seqIdColumn source_id
Thu Dec 8 09:04:53 2005 ARG seqSoTerm
Thu Dec 8 09:04:53 2005 ARG seqType
Thu Dec 8 09:04:53 2005 ARG soCvsVersion
Thu Dec 8 09:04:53 2005 ARG sqlVerbose 0
Thu Dec 8 09:04:53 2005 ARG testNumber
Thu Dec 8 09:04:53 2005 ARG user
Thu Dec 8 09:04:53 2005 ARG verbose 0
Thu Dec 8 09:04:53 2005 ARG veryVerbose 0
Thu Dec 8 09:04:53 2005 AlgInvocationId 30
Thu Dec 8 09:04:53 2005 COMMIT commit on
Thu Dec 8 09:04:55 2005 Processing file 'kinetoplastida_nt'...
DBD::Pg::st execute failed: ERROR: cannot insert into a view
HINT: You need an unconditional ON INSERT DO INSTEAD rule.
ERROR:
SQL ERROR!! involving
Values: 4 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b=
0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} Values: 4') called at
/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa90=
4b0)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY(0xa148314)') call=
ed
at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1813
GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1680
GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
731
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
330
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'HASH(0xabe05b0)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'ARRAY(0x9c96700)') called at /GUS/gus_home/bin/ga line 11
STACK TRACE:
at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b=
0)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} Values: 4') called at
/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa90=
4b0)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY(0xa148314)') call=
ed
at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1813
GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1680
GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
731
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
330
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'HASH(0xabe05b0)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x9c82c20)',
'ARRAY(0x9c96700)') called at /GUS/gus_home/bin/ga line 11
Could you help me ?
thanks again,
Ricardo Balbi
2005/12/7, Mark S. Heiges <mh...@ug...>:
>
> One short term solution is to adjust your local schema "alter table
> SRes.Reference modify (author varchar2(4000))", or something like
> that, and then restart the loading.
>
> You can also file a feature request in the GUS Schema issue tracker
> to increase that column in a future release - https://
> www.cbil.upenn.edu/tracker.
>
> On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote:
>
> > Hi,
> >
> > I am trying to load kinetoplastida_nt, using
> > InsertSequenceFeatures plugin. But I am not obtaining.
> > Kinetoplastida_nt has a register whose author field exceeds the
> > maximum size the table sres.reference.
> >
> > How I must proceed to load this base?
> >
> > It follows below the error:
> >
> > [rbalbi1@crithidia bancos]$ ga
> > GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/
> > config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt --
> > fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer
> > "2005-12-06" --commit
> > Tue Dec 6 21:32:42 2005 ARG algoinvo 1
> > Tue Dec 6 21:32:42 2005 ARG comment
> > Tue Dec 6 21:32:42 2005 ARG commit 1
> > Tue Dec 6 21:32:42 2005 ARG debug 0
> > Tue Dec 6 21:32:42 2005 ARG defaultOrganism
> > Tue Dec 6 21:32:42 2005 ARG extDbName
> > Kinetoplastida_nt
> > Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06
> > Tue Dec 6 21:32:42 2005 ARG fileFormat genbank
> > Tue Dec 6 21:32:42 2005 ARG gff2GroupTag
> > Tue Dec 6 21:32:42 2005 ARG group
> > Tue Dec 6 21:32:42 2005 ARG gusconfigfile /GUS/
> > gus_home/config/gus.config
> > Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs
> > Tue Dec 6 21:32:42 2005 ARG help
> > Tue Dec 6 21:32:42 2005 ARG helpHTML
> > Tue Dec 6 21:32:42 2005 ARG inputFileExtension
> > Tue Dec 6 21:32:42 2005 ARG inputFileOrDir
> > kinetoplastida_nt
> > Tue Dec 6 21:32:42 2005 ARG makeSourceids
> > Tue Dec 6 21:32:42 2005 ARG mapFile /GUS/gus_home/
> > config/genbank2gus.xml
> > Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass
> > Tue Dec 6 21:32:42 2005 ARG project
> > Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id
> > Tue Dec 6 21:32:42 2005 ARG seqSoTerm
> > Tue Dec 6 21:32:42 2005 ARG seqType
> > Tue Dec 6 21:32:42 2005 ARG soCvsVersion
> > Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0
> > Tue Dec 6 21:32:42 2005 ARG testNumber
> > Tue Dec 6 21:32:42 2005 ARG user
> > Tue Dec 6 21:32:42 2005 ARG verbose 0
> > Tue Dec 6 21:32:42 2005 ARG veryVerbose 0
> > Tue Dec 6 21:32:42 2005 AlgInvocationId 26
> > Tue Dec 6 21:32:42 2005 COMMIT commit on
> > Tue Dec 6 21:32:44 2005 Processing file 'kinetoplastida_nt'...
> > DBD::Pg::st execute failed: ERROR: value too long for type
> > character varying(1000)
> >
> > ERROR:
> >
> > SQL ERROR!! involving
> >
> > INSERT INTO SRes.Reference ( journal_or_book_name,
> > group_write, other_read, group_read, author, user_read,
> > row_user_id, reference_id, modification_date, other_write,
> > row_alg_invocation_id, row_project_id, row_group_id, title,
> > user_write )
> > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? )
> > Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1,
> > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D.,
> > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L.,
> > Blandin,G., Westenberger,S.J., Caler,E., Cerqueira,G.C.,
> > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P.,
> > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A.,
> > Carrington,M., Crabtree,J., Darban,H., da Silveira,J.F., de
> > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T.,
> > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y.,
> > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D.,
> > Levin,M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R.,
> > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S.,
> > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M.,
> > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg,S.L., Sanchez,D.O.,
> > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T.,
> > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N.,
> > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart,K.D. and
> > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of
> > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/
> > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
> > GUS::ObjRelP::DbiDbHandle::death
> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)', '\x{a} SQL ERROR!!
> > involving\x{a} \x{a} INSERT INTO SRes.Reference ( j...') called
> > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
> > GUS::ObjRelP::DbiDbHandle::sqlExec
> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)',
> > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x8e826cc)', 'ARRAY
> > (0x8e82708)', '\x{a} INSERT INTO SRes.Reference
> > ( journal_or_book_name, grou...') called at /GUS/gus_home/lib/perl/
> > GUS/ObjRelP/DbiRow.pm line 666
> > GUS::ObjRelP::DbiRow::quote_and_insert
> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)', 'HASH(0x9889d48)')
> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
> > GUS::ObjRelP::DbiRow::insert
> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)') called at /GUS/
> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
> >
> >
> > thanks,
> > Ricardo
>
>
|
|
From: Mark S. H. <mh...@ug...> - 2005-12-07 02:38:54
|
One short term solution is to adjust your local schema "alter table SRes.Reference modify (author varchar2(4000))", or something like that, and then restart the loading. You can also file a feature request in the GUS Schema issue tracker to increase that column in a future release - https:// www.cbil.upenn.edu/tracker. On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote: > Hi, > > I am trying to load kinetoplastida_nt, using > InsertSequenceFeatures plugin. But I am not obtaining. > Kinetoplastida_nt has a register whose author field exceeds the > maximum size the table sres.reference. > > How I must proceed to load this base? > > It follows below the error: > > [rbalbi1@crithidia bancos]$ ga > GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/ > config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt -- > fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer > "2005-12-06" --commit > Tue Dec 6 21:32:42 2005 ARG algoinvo 1 > Tue Dec 6 21:32:42 2005 ARG comment > Tue Dec 6 21:32:42 2005 ARG commit 1 > Tue Dec 6 21:32:42 2005 ARG debug 0 > Tue Dec 6 21:32:42 2005 ARG defaultOrganism > Tue Dec 6 21:32:42 2005 ARG extDbName > Kinetoplastida_nt > Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06 > Tue Dec 6 21:32:42 2005 ARG fileFormat genbank > Tue Dec 6 21:32:42 2005 ARG gff2GroupTag > Tue Dec 6 21:32:42 2005 ARG group > Tue Dec 6 21:32:42 2005 ARG gusconfigfile /GUS/ > gus_home/config/gus.config > Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs > Tue Dec 6 21:32:42 2005 ARG help > Tue Dec 6 21:32:42 2005 ARG helpHTML > Tue Dec 6 21:32:42 2005 ARG inputFileExtension > Tue Dec 6 21:32:42 2005 ARG inputFileOrDir > kinetoplastida_nt > Tue Dec 6 21:32:42 2005 ARG makeSourceids > Tue Dec 6 21:32:42 2005 ARG mapFile /GUS/gus_home/ > config/genbank2gus.xml > Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass > Tue Dec 6 21:32:42 2005 ARG project > Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id > Tue Dec 6 21:32:42 2005 ARG seqSoTerm > Tue Dec 6 21:32:42 2005 ARG seqType > Tue Dec 6 21:32:42 2005 ARG soCvsVersion > Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0 > Tue Dec 6 21:32:42 2005 ARG testNumber > Tue Dec 6 21:32:42 2005 ARG user > Tue Dec 6 21:32:42 2005 ARG verbose 0 > Tue Dec 6 21:32:42 2005 ARG veryVerbose 0 > Tue Dec 6 21:32:42 2005 AlgInvocationId 26 > Tue Dec 6 21:32:42 2005 COMMIT commit on > Tue Dec 6 21:32:44 2005 Processing file 'kinetoplastida_nt'... > DBD::Pg::st execute failed: ERROR: value too long for type > character varying(1000) > > ERROR: > > SQL ERROR!! involving > > INSERT INTO SRes.Reference ( journal_or_book_name, > group_write, other_read, group_read, author, user_read, > row_user_id, reference_id, modification_date, other_write, > row_alg_invocation_id, row_project_id, row_group_id, title, > user_write ) > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? ) > Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1, > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D., > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L., > Blandin,G., Westenberger,S.J., Caler,E., Cerqueira,G.C., > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P., > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A., > Carrington,M., Crabtree,J., Darban,H., da Silveira,J.F., de > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T., > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y., > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D., > Levin,M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R., > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S., > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M., > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg,S.L., Sanchez,D.O., > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T., > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N., > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart,K.D. and > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/ > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 > GUS::ObjRelP::DbiDbHandle::death > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)', '\x{a} SQL ERROR!! > involving\x{a} \x{a} INSERT INTO SRes.Reference ( j...') called > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 > GUS::ObjRelP::DbiDbHandle::sqlExec > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)', > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8e826cc)', 'ARRAY > (0x8e82708)', '\x{a} INSERT INTO SRes.Reference > ( journal_or_book_name, grou...') called at /GUS/gus_home/lib/perl/ > GUS/ObjRelP/DbiRow.pm line 666 > GUS::ObjRelP::DbiRow::quote_and_insert > ('GUS::Model::SRes::Reference=HASH(0x987901c)', 'HASH(0x9889d48)') > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613 > GUS::ObjRelP::DbiRow::insert > ('GUS::Model::SRes::Reference=HASH(0x987901c)') called at /GUS/ > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 > > > thanks, > Ricardo |
|
From: Ricardo B. <rb...@gm...> - 2005-12-06 23:48:49
|
Hi,
I am trying to load kinetoplastida_nt, using InsertSequenceFeatures
plugin. But I am not obtaining.
Kinetoplastida_nt has a register whose author field exceeds the maximum
size the table sres.reference.
How I must proceed to load this base?
It follows below the error:
[rbalbi1@crithidia bancos]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
$GUS_HOME/config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt
--fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer
"2005-12-06" --commit
Tue Dec 6 21:32:42 2005 ARG algoinvo 1
Tue Dec 6 21:32:42 2005 ARG comment
Tue Dec 6 21:32:42 2005 ARG commit 1
Tue Dec 6 21:32:42 2005 ARG debug 0
Tue Dec 6 21:32:42 2005 ARG defaultOrganism
Tue Dec 6 21:32:42 2005 ARG extDbName Kinetoplastida_nt
Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06
Tue Dec 6 21:32:42 2005 ARG fileFormat genbank
Tue Dec 6 21:32:42 2005 ARG gff2GroupTag
Tue Dec 6 21:32:42 2005 ARG group
Tue Dec 6 21:32:42 2005 ARG gusconfigfile
/GUS/gus_home/config/gus.config
Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs
Tue Dec 6 21:32:42 2005 ARG help
Tue Dec 6 21:32:42 2005 ARG helpHTML
Tue Dec 6 21:32:42 2005 ARG inputFileExtension
Tue Dec 6 21:32:42 2005 ARG inputFileOrDir kinetoplastida_nt
Tue Dec 6 21:32:42 2005 ARG makeSourceids
Tue Dec 6 21:32:42 2005 ARG mapFile
/GUS/gus_home/config/genbank2gus.xml
Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass
Tue Dec 6 21:32:42 2005 ARG project
Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id
Tue Dec 6 21:32:42 2005 ARG seqSoTerm
Tue Dec 6 21:32:42 2005 ARG seqType
Tue Dec 6 21:32:42 2005 ARG soCvsVersion
Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0
Tue Dec 6 21:32:42 2005 ARG testNumber
Tue Dec 6 21:32:42 2005 ARG user
Tue Dec 6 21:32:42 2005 ARG verbose 0
Tue Dec 6 21:32:42 2005 ARG veryVerbose 0
Tue Dec 6 21:32:42 2005 AlgInvocationId 26
Tue Dec 6 21:32:42 2005 COMMIT commit on
Tue Dec 6 21:32:44 2005 Processing file 'kinetoplastida_nt'...
DBD::Pg::st execute failed: ERROR: value too long for type character
varying(1000)
ERROR:
SQL ERROR!! involving
INSERT INTO SRes.Reference ( journal_or_book_name, group_write,
other_read, group_read, author, user_read, row_user_id, reference_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, title, user_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? )
Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1, 1, 1,
El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D., Aggarwal,G., Tran,
A.N., Ghedin,E., Worthey,E.A., Delcher,A.L., Blandin,G., Westenberger,S.J.,
Caler,E., Cerqueira,G.C., Branche,C., Haas,B., Anupama,A., Arner,E.,
Aslund,L., Attipoe,P., Bontempi,E., Bringaud,F., Burton,P., Cadag,E.,
Campbell,D.A., Carrington,M., Crabtree,J., Darban,H., da Silveira,J.F., de
Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T., Ferella,M.,
Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y., Kindlund,E., Klingbeil,M.,
Kluge,S., Koo,H., Lacerda,D., Levin,M.J., Lorenzi,H., Louie,T., Machado,C.R=
.,
McCulloch,R., McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S.,
Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M., Ramirez=
,
J.L., Rinta,J., Robertson,L., Salzberg,S.L., Sanchez,D.O., Seyler,A.,
Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T., Tarleton,R.,
Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N., Wickstead,B., Wortman,J.,
White,O., Fraser,C.M., Stuart,K.D. and Andersson,B., 1, 1, 6, 0, 26, 1, 1,
The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease=
,
1 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d1=
4)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO SRes.Reference (
j...') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4=
d14)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x8e826cc)', 'ARRAY(0x8e82708)',
'\x{a} INSERT INTO SRes.Reference ( journal_or_book_name, grou...')
called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::Reference=3DHASH(=
0x987901c)',
'HASH(0x9889d48)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 613
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::Reference=3DHASH(0x987901c)=
')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
thanks,
Ricardo
|
|
From: Michael S. <msa...@pc...> - 2005-12-01 19:39:18
|
No guarantees, but you can grab it here: https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/DBAdmin/bin/ dbaDeinstallGus I believe that it does have dependencies on other things that have been updated in GUS since the downloadable release. At least you can look at the code and see what it's doing-- pretty trivial. --Mike On Dec 1, 2005, at 2:12 PM, Chris Topinka wrote: > Apparently I didn't get it in the distribution I downloaded from > the GUS site. > This is my bin dir: > > [oracle@ws17 bin]$ pwd > /home/oracle/GUS/gus_home/bin > [oracle@ws17 bin]$ ls > benchmarkQueries.pl getSubTaxa rebuildIndexes.pl > checkForeignKeysIndexed.pl gobuild runBlastSim4.pl > checkTableInfo.pl grantPermissions.pl runGoSimilarities > dbaDumpSchema gusDeleteRows showConstraints.pl > dumpTable.pl gusExtractSequences singleCoverage.pl > extractHits.pl hierAnatomyDemo.pl updateDbESTMirror.pl > genbankFileFilter hifytojava versionEntries.pl > generateAAFilterFile loadDbESTMirror.pl > > > Is it one of these? > > Is there a way I can get it without downloading the whole thing? > > Chris > > On 12/1/05, Michael Saffitz <msa...@pc...> wrote: > Hi Chris: > > dbaDeinstallGus is in the trunk of the repository, it's installed > with GUS in $GUS_HOME/bin > > You can always just do a drop user dots, drop user ... and so on, but > the utility is much faster and makes sure you didn't miss anything. > > --Mike > > On Dec 1, 2005, at 1:32 PM, Chris Topinka wrote: > > > where can I find the Deinstall script? Is there a way to just > > manually remove users/groups/tables from Oracle that conflict? > > > > thanks, > > > > chris > > > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > Sorry. You'll have to back out the previous install before you try > > again. You can use the dbaDeinstallGus utility to do this (but be > > careful and read the warnings-- it will delete data). > > > > --Mike > > > > On Nov 29, 2005, at 1:20 PM, Chris Topinka wrote: > > > > > after creating GUS tablespace I get... > > > > > > BUILD FAILED > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > error occurred while executing this line: > > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > > java.io.IOException: Error executing SQL: ' > > > CREATE USER TESSVer IDENTIFIED BY temppass PASSWORD EXPIRE ACCOUNT > > > LOCK QUOTA UNLIMITED ON USERS DEFAULT TABLESPACE USERS' Error: > > > ORA-01920: user name 'TESSVER' conflicts with another user or role > > > name > > > > > > > > > Thanks. > > > > > > > > > > > > On 11/29/05, Michael Saffitz < msa...@pc...> wrote: > > > Hi Chris, > > > > > > Ok, you're almost there. Either: > > > > > > 1) Create a GUS tablespace > > > 2) Update your gus_schema.xml file (in $PROJECT_HOME/GusSchema/ > > > Definition/config) to use tablespace="USERS" (or whatever) > > instead of > > > GUS. > > > > > > --Mike > > > > > > On Nov 29, 2005, at 12:37 PM, Chris Topinka wrote: > > > > > > > How should I reply? > > > > > > > > Ok. now I get... > > > > > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > > org.gusdb.schema.InstallSchemaTask execute > > > > [InstallSchema] INFO: Reading database from /home/oracle/GUS/ > > > > project_home/GUS/Schema/gus_schema.xml > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > > org.gusdb.dbadmin.reader.SchemaReader doRead > > > > [InstallSchema] INFO: Reading Database > > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > > org.gusdb.dbadmin.model.Database resolveReferences > > > > [InstallSchema] INFO: Resolving Database References > > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > > [InstallSchema] INFO: Validating Database: 'null' > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.schema.InstallSchemaTask setTablespace > > > > [InstallSchema] INFO: Setting tablespaces to GUS > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > > [InstallSchema] INFO: Validating Database: 'null' > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > > [InstallSchema] INFO: Writing Database > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > > [InstallSchema] INFO: Validating Database: 'null' > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > > [InstallSchema] INFO: Writing Database > > > > > > > > BUILD FAILED > > > > /home/oracle/GUS/project_home/install/build.xml:28: The > following > > > > error occurred while executing this line: > > > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > > > java.io.IOException : Error executing SQL: ' > > > > ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: > > > > tablespace 'GUS' does not exist > > > > > > > > > > > > what is this last line? > > > > > > > > On 11/29/05, Michael Saffitz < msa...@pc... > wrote: > > > > Hi Chris, > > > > > > > > Don't use the sys account. Use another account that has been > > > granted > > > > dba privileges. > > > > > > > > --Mike > > > > > > > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > > > > > > > when I run build I get... > > > > > > > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > > > > org.gusdb.schema.InstallSchemaTask initialize > > > > > [InstallSchema] SEVERE: Unable to connect to database. > > > > > DSN=' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu: > 1521 :WS17' > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: > connection to > > > sys > > > > > should be as sysdba or sysoper > > > > > [InstallSchema] at > > > > > oracle.jdbc.driver.DatabaseError.throwSqlException > > > > > (DatabaseError.java :124) > > > > > [InstallSchema] at > > > oracle.jdbc.driver.T4CTTIoer.processError > > > > > (T4CTTIoer.java:304) > > > > > [InstallSchema] at > > > oracle.jdbc.driver.T4CTTIoer.processError > > > > > ( T4CTTIoer.java:271) > > > > > . > > > > > . > > > > > . > > > > > . > > > > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > > > > (Main.java:187) > > > > > [InstallSchema] at > > > org.apache.tools.ant.launch.Launcher.run > > > > > (Launcher.java:246) > > > > > [InstallSchema] at > > > org.apache.tools.ant.launch.Launcher.main > > > > > (Launcher.java:67) > > > > > > > > > > BUILD FAILED > > > > > /home/oracle/GUS/project_home/install/build.xml:28: The > > following > > > > > error occurred while executing this line: > > > > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to > > connect > > > > > to database > > > > > > > > > > Total time: 7 seconds > > > > > > > > > > > > > > > My gus.config looks like this: > > > > > > > > > > dbVendor=Oracle > > > > > dbiDsn=dbi:Oracle: ws17.itcomplab.missouri.edu > > > > > jdbcDsn= jdbc:oracle:thin:@ws17.itcomplab.missouri.edu : > > 1521 :WS17 > > > > > > > > > > > > > > > # Login and Password to the RDBMS > > > > > > > > > > databaseLogin=sys > > > > > databasePassword=adminws17 > > > > > > > > > > # Username, group, and project info from the relevant Core > > tables > > > > > > > > > > userName=sys > > > > > group=sysdba > > > > > project=Database administration > > > > > > > > > > tablespace=GUS > > > > > > > > > > Any suggestions? The line: > > > > > > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: > connection to > > > sys > > > > > should be as sysdba or sysoper > > > > > > > > > > seems to be the problem. How should I change config? > > > > > > > > > > Thanks, > > > > > > > > > > chris > > > > > > > > > > > > > > > -- > > > > > Christopher M. Topinka > > > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > > > 113 Life Sciences Center > > > > > University of Missouri > > > > > Columbia, MO 65211 > > > > > (573)-823-0616 > > > > > cmt...@mi... > > > > > > > > > > > > > > > > > > > > -- > > > > Christopher M. Topinka > > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > > 113 Life Sciences Center > > > > University of Missouri > > > > Columbia, MO 65211 > > > > (573)-823-0616 > > > > cmt...@mi... > > > > > > > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > MU ACM Student Chapter 2005-2006 Program Chair > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > MU ACM Student Chapter 2005-2006 Program Chair > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... |
|
From: Chris T. <cmt...@gm...> - 2005-12-01 19:20:23
|
when I browse svn under gusTrunk I can't see any of the files. Is there a reason for this? -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science MU ACM Student Chapter 2005-2006 Program Chair University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
|
From: Chris T. <cmt...@gm...> - 2005-12-01 19:13:02
|
Apparently I didn't get it in the distribution I downloaded from the GUS site. This is my bin dir: [oracle@ws17 bin]$ pwd /home/oracle/GUS/gus_home/bin [oracle@ws17 bin]$ ls benchmarkQueries.pl getSubTaxa rebuildIndexes.pl checkForeignKeysIndexed.pl gobuild runBlastSim4.pl checkTableInfo.pl grantPermissions.pl runGoSimilarities dbaDumpSchema gusDeleteRows showConstraints.pl dumpTable.pl gusExtractSequences singleCoverage.pl extractHits.pl hierAnatomyDemo.pl updateDbESTMirror.pl genbankFileFilter hifytojava versionEntries.pl generateAAFilterFile loadDbESTMirror.pl Is it one of these? Is there a way I can get it without downloading the whole thing? Chris On 12/1/05, Michael Saffitz <msa...@pc...> wrote: > > > Hi Chris: > > dbaDeinstallGus is in the trunk of the repository, it's installed > with GUS in $GUS_HOME/bin > > You can always just do a drop user dots, drop user ... and so on, but > the utility is much faster and makes sure you didn't miss anything. > > --Mike > > On Dec 1, 2005, at 1:32 PM, Chris Topinka wrote: > > > where can I find the Deinstall script? Is there a way to just > > manually remove users/groups/tables from Oracle that conflict? > > > > thanks, > > > > chris > > > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > Sorry. You'll have to back out the previous install before you try > > again. You can use the dbaDeinstallGus utility to do this (but be > > careful and read the warnings-- it will delete data). > > > > --Mike > > > > On Nov 29, 2005, at 1:20 PM, Chris Topinka wrote: > > > > > after creating GUS tablespace I get... > > > > > > BUILD FAILED > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > error occurred while executing this line: > > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > > java.io.IOException: Error executing SQL: ' > > > CREATE USER TESSVer IDENTIFIED BY temppass PASSWORD EXPIRE ACCOUNT > > > LOCK QUOTA UNLIMITED ON USERS DEFAULT TABLESPACE USERS' Error: > > > ORA-01920: user name 'TESSVER' conflicts with another user or role > > > name > > > > > > > > > Thanks. > > > > > > > > > > > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > > Hi Chris, > > > > > > Ok, you're almost there. Either: > > > > > > 1) Create a GUS tablespace > > > 2) Update your gus_schema.xml file (in $PROJECT_HOME/GusSchema/ > > > Definition/config) to use tablespace=3D"USERS" (or whatever) > > instead of > > > GUS. > > > > > > --Mike > > > > > > On Nov 29, 2005, at 12:37 PM, Chris Topinka wrote: > > > > > > > How should I reply? > > > > > > > > Ok. now I get... > > > > > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > > org.gusdb.schema.InstallSchemaTask execute > > > > [InstallSchema] INFO: Reading database from /home/oracle/GUS/ > > > > project_home/GUS/Schema/gus_schema.xml > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > > org.gusdb.dbadmin.reader.SchemaReader doRead > > > > [InstallSchema] INFO: Reading Database > > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > > org.gusdb.dbadmin.model.Database resolveReferences > > > > [InstallSchema] INFO: Resolving Database References > > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > > [InstallSchema] INFO: Validating Database: 'null' > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.schema.InstallSchemaTask setTablespace > > > > [InstallSchema] INFO: Setting tablespaces to GUS > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > > [InstallSchema] INFO: Validating Database: 'null' > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > > [InstallSchema] INFO: Writing Database > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > > [InstallSchema] INFO: Validating Database: 'null' > > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > > [InstallSchema] INFO: Writing Database > > > > > > > > BUILD FAILED > > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > > error occurred while executing this line: > > > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > > > java.io.IOException : Error executing SQL: ' > > > > ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: > > > > tablespace 'GUS' does not exist > > > > > > > > > > > > what is this last line? > > > > > > > > On 11/29/05, Michael Saffitz < msa...@pc... > wrote: > > > > Hi Chris, > > > > > > > > Don't use the sys account. Use another account that has been > > > granted > > > > dba privileges. > > > > > > > > --Mike > > > > > > > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > > > > > > > when I run build I get... > > > > > > > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > > > > org.gusdb.schema.InstallSchemaTask initialize > > > > > [InstallSchema] SEVERE: Unable to connect to database. > > > > > DSN=3D' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17' > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > > > sys > > > > > should be as sysdba or sysoper > > > > > [InstallSchema] at > > > > > oracle.jdbc.driver.DatabaseError.throwSqlException > > > > > (DatabaseError.java:124) > > > > > [InstallSchema] at > > > oracle.jdbc.driver.T4CTTIoer.processError > > > > > (T4CTTIoer.java:304) > > > > > [InstallSchema] at > > > oracle.jdbc.driver.T4CTTIoer.processError > > > > > ( T4CTTIoer.java:271) > > > > > . > > > > > . > > > > > . > > > > > . > > > > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > > > > (Main.java:187) > > > > > [InstallSchema] at > > > org.apache.tools.ant.launch.Launcher.run > > > > > (Launcher.java:246) > > > > > [InstallSchema] at > > > org.apache.tools.ant.launch.Launcher.main > > > > > (Launcher.java:67) > > > > > > > > > > BUILD FAILED > > > > > /home/oracle/GUS/project_home/install/build.xml:28: The > > following > > > > > error occurred while executing this line: > > > > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to > > connect > > > > > to database > > > > > > > > > > Total time: 7 seconds > > > > > > > > > > > > > > > My gus.config looks like this: > > > > > > > > > > dbVendor=3DOracle > > > > > dbiDsn=3Ddbi:Oracle: ws17.itcomplab.missouri.edu > > > > > jdbcDsn=3D jdbc:oracle:thin:@ws17.itcomplab.missouri.edu: > > 1521 :WS17 > > > > > > > > > > > > > > > # Login and Password to the RDBMS > > > > > > > > > > databaseLogin=3Dsys > > > > > databasePassword=3Dadminws17 > > > > > > > > > > # Username, group, and project info from the relevant Core > > tables > > > > > > > > > > userName=3Dsys > > > > > group=3Dsysdba > > > > > project=3DDatabase administration > > > > > > > > > > tablespace=3DGUS > > > > > > > > > > Any suggestions? The line: > > > > > > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > > > sys > > > > > should be as sysdba or sysoper > > > > > > > > > > seems to be the problem. How should I change config? > > > > > > > > > > Thanks, > > > > > > > > > > chris > > > > > > > > > > > > > > > -- > > > > > Christopher M. Topinka > > > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > > > 113 Life Sciences Center > > > > > University of Missouri > > > > > Columbia, MO 65211 > > > > > (573)-823-0616 > > > > > cmt...@mi... > > > > > > > > > > > > > > > > > > > > -- > > > > Christopher M. Topinka > > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > > 113 Life Sciences Center > > > > University of Missouri > > > > Columbia, MO 65211 > > > > (573)-823-0616 > > > > cmt...@mi... > > > > > > > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > MU ACM Student Chapter 2005-2006 Program Chair > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science MU ACM Student Chapter 2005-2006 Program Chair University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
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From: Michael S. <msa...@pc...> - 2005-12-01 18:50:14
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Hi Chris: dbaDeinstallGus is in the trunk of the repository, it's installed with GUS in $GUS_HOME/bin You can always just do a drop user dots, drop user ... and so on, but the utility is much faster and makes sure you didn't miss anything. --Mike On Dec 1, 2005, at 1:32 PM, Chris Topinka wrote: > where can I find the Deinstall script? Is there a way to just > manually remove users/groups/tables from Oracle that conflict? > > thanks, > > chris > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > Sorry. You'll have to back out the previous install before you try > again. You can use the dbaDeinstallGus utility to do this (but be > careful and read the warnings-- it will delete data). > > --Mike > > On Nov 29, 2005, at 1:20 PM, Chris Topinka wrote: > > > after creating GUS tablespace I get... > > > > BUILD FAILED > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > error occurred while executing this line: > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > java.io.IOException: Error executing SQL: ' > > CREATE USER TESSVer IDENTIFIED BY temppass PASSWORD EXPIRE ACCOUNT > > LOCK QUOTA UNLIMITED ON USERS DEFAULT TABLESPACE USERS' Error: > > ORA-01920: user name 'TESSVER' conflicts with another user or role > > name > > > > > > Thanks. > > > > > > > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > Hi Chris, > > > > Ok, you're almost there. Either: > > > > 1) Create a GUS tablespace > > 2) Update your gus_schema.xml file (in $PROJECT_HOME/GusSchema/ > > Definition/config) to use tablespace="USERS" (or whatever) > instead of > > GUS. > > > > --Mike > > > > On Nov 29, 2005, at 12:37 PM, Chris Topinka wrote: > > > > > How should I reply? > > > > > > Ok. now I get... > > > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > org.gusdb.schema.InstallSchemaTask execute > > > [InstallSchema] INFO: Reading database from /home/oracle/GUS/ > > > project_home/GUS/Schema/gus_schema.xml > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > org.gusdb.dbadmin.reader.SchemaReader doRead > > > [InstallSchema] INFO: Reading Database > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > org.gusdb.dbadmin.model.Database resolveReferences > > > [InstallSchema] INFO: Resolving Database References > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > [InstallSchema] INFO: Validating Database: 'null' > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.schema.InstallSchemaTask setTablespace > > > [InstallSchema] INFO: Setting tablespaces to GUS > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > [InstallSchema] INFO: Validating Database: 'null' > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > [InstallSchema] INFO: Writing Database > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > [InstallSchema] INFO: Validating Database: 'null' > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > [InstallSchema] INFO: Writing Database > > > > > > BUILD FAILED > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > error occurred while executing this line: > > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > > java.io.IOException : Error executing SQL: ' > > > ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: > > > tablespace 'GUS' does not exist > > > > > > > > > what is this last line? > > > > > > On 11/29/05, Michael Saffitz < msa...@pc... > wrote: > > > Hi Chris, > > > > > > Don't use the sys account. Use another account that has been > > granted > > > dba privileges. > > > > > > --Mike > > > > > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > > > > > when I run build I get... > > > > > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > > > org.gusdb.schema.InstallSchemaTask initialize > > > > [InstallSchema] SEVERE: Unable to connect to database. > > > > DSN=' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17' > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > > sys > > > > should be as sysdba or sysoper > > > > [InstallSchema] at > > > > oracle.jdbc.driver.DatabaseError.throwSqlException > > > > (DatabaseError.java:124) > > > > [InstallSchema] at > > oracle.jdbc.driver.T4CTTIoer.processError > > > > (T4CTTIoer.java:304) > > > > [InstallSchema] at > > oracle.jdbc.driver.T4CTTIoer.processError > > > > ( T4CTTIoer.java:271) > > > > . > > > > . > > > > . > > > > . > > > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > > > (Main.java:187) > > > > [InstallSchema] at > > org.apache.tools.ant.launch.Launcher.run > > > > (Launcher.java:246) > > > > [InstallSchema] at > > org.apache.tools.ant.launch.Launcher.main > > > > (Launcher.java:67) > > > > > > > > BUILD FAILED > > > > /home/oracle/GUS/project_home/install/build.xml:28: The > following > > > > error occurred while executing this line: > > > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to > connect > > > > to database > > > > > > > > Total time: 7 seconds > > > > > > > > > > > > My gus.config looks like this: > > > > > > > > dbVendor=Oracle > > > > dbiDsn=dbi:Oracle: ws17.itcomplab.missouri.edu > > > > jdbcDsn= jdbc:oracle:thin:@ws17.itcomplab.missouri.edu: > 1521 :WS17 > > > > > > > > > > > > # Login and Password to the RDBMS > > > > > > > > databaseLogin=sys > > > > databasePassword=adminws17 > > > > > > > > # Username, group, and project info from the relevant Core > tables > > > > > > > > userName=sys > > > > group=sysdba > > > > project=Database administration > > > > > > > > tablespace=GUS > > > > > > > > Any suggestions? The line: > > > > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > > sys > > > > should be as sysdba or sysoper > > > > > > > > seems to be the problem. How should I change config? > > > > > > > > Thanks, > > > > > > > > chris > > > > > > > > > > > > -- > > > > Christopher M. Topinka > > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > > 113 Life Sciences Center > > > > University of Missouri > > > > Columbia, MO 65211 > > > > (573)-823-0616 > > > > cmt...@mi... > > > > > > > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > MU ACM Student Chapter 2005-2006 Program Chair > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... |
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From: Chris T. <cmt...@gm...> - 2005-12-01 18:32:15
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where can I find the Deinstall script? Is there a way to just manually remove users/groups/tables from Oracle that conflict? thanks, chris On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > > Sorry. You'll have to back out the previous install before you try > again. You can use the dbaDeinstallGus utility to do this (but be > careful and read the warnings-- it will delete data). > > --Mike > > On Nov 29, 2005, at 1:20 PM, Chris Topinka wrote: > > > after creating GUS tablespace I get... > > > > BUILD FAILED > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > error occurred while executing this line: > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > java.io.IOException: Error executing SQL: ' > > CREATE USER TESSVer IDENTIFIED BY temppass PASSWORD EXPIRE ACCOUNT > > LOCK QUOTA UNLIMITED ON USERS DEFAULT TABLESPACE USERS' Error: > > ORA-01920: user name 'TESSVER' conflicts with another user or role > > name > > > > > > Thanks. > > > > > > > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > Hi Chris, > > > > Ok, you're almost there. Either: > > > > 1) Create a GUS tablespace > > 2) Update your gus_schema.xml file (in $PROJECT_HOME/GusSchema/ > > Definition/config) to use tablespace=3D"USERS" (or whatever) instead of > > GUS. > > > > --Mike > > > > On Nov 29, 2005, at 12:37 PM, Chris Topinka wrote: > > > > > How should I reply? > > > > > > Ok. now I get... > > > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > org.gusdb.schema.InstallSchemaTask execute > > > [InstallSchema] INFO: Reading database from /home/oracle/GUS/ > > > project_home/GUS/Schema/gus_schema.xml > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > > org.gusdb.dbadmin.reader.SchemaReader doRead > > > [InstallSchema] INFO: Reading Database > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > org.gusdb.dbadmin.model.Database resolveReferences > > > [InstallSchema] INFO: Resolving Database References > > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > [InstallSchema] INFO: Validating Database: 'null' > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.schema.InstallSchemaTask setTablespace > > > [InstallSchema] INFO: Setting tablespaces to GUS > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > [InstallSchema] INFO: Validating Database: 'null' > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > [InstallSchema] INFO: Writing Database > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.util.DatabaseValidator validate > > > [InstallSchema] INFO: Validating Database: 'null' > > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > > org.gusdb.dbadmin.writer.SchemaWriter write > > > [InstallSchema] INFO: Writing Database > > > > > > BUILD FAILED > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > error occurred while executing this line: > > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > > java.io.IOException : Error executing SQL: ' > > > ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: > > > tablespace 'GUS' does not exist > > > > > > > > > what is this last line? > > > > > > On 11/29/05, Michael Saffitz < msa...@pc...> wrote: > > > Hi Chris, > > > > > > Don't use the sys account. Use another account that has been > > granted > > > dba privileges. > > > > > > --Mike > > > > > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > > > > > when I run build I get... > > > > > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > > > org.gusdb.schema.InstallSchemaTask initialize > > > > [InstallSchema] SEVERE: Unable to connect to database. > > > > DSN=3D' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17' > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > > sys > > > > should be as sysdba or sysoper > > > > [InstallSchema] at > > > > oracle.jdbc.driver.DatabaseError.throwSqlException > > > > (DatabaseError.java:124) > > > > [InstallSchema] at > > oracle.jdbc.driver.T4CTTIoer.processError > > > > (T4CTTIoer.java:304) > > > > [InstallSchema] at > > oracle.jdbc.driver.T4CTTIoer.processError > > > > ( T4CTTIoer.java:271) > > > > . > > > > . > > > > . > > > > . > > > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > > > (Main.java:187) > > > > [InstallSchema] at > > org.apache.tools.ant.launch.Launcher.run > > > > (Launcher.java:246) > > > > [InstallSchema] at > > org.apache.tools.ant.launch.Launcher.main > > > > (Launcher.java:67) > > > > > > > > BUILD FAILED > > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > > error occurred while executing this line: > > > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect > > > > to database > > > > > > > > Total time: 7 seconds > > > > > > > > > > > > My gus.config looks like this: > > > > > > > > dbVendor=3DOracle > > > > dbiDsn=3Ddbi:Oracle: ws17.itcomplab.missouri.edu > > > > jdbcDsn=3Djdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17 > > > > > > > > > > > > # Login and Password to the RDBMS > > > > > > > > databaseLogin=3Dsys > > > > databasePassword=3Dadminws17 > > > > > > > > # Username, group, and project info from the relevant Core tables > > > > > > > > userName=3Dsys > > > > group=3Dsysdba > > > > project=3DDatabase administration > > > > > > > > tablespace=3DGUS > > > > > > > > Any suggestions? The line: > > > > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > > sys > > > > should be as sysdba or sysoper > > > > > > > > seems to be the problem. How should I change config? > > > > > > > > Thanks, > > > > > > > > chris > > > > > > > > > > > > -- > > > > Christopher M. Topinka > > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > > 113 Life Sciences Center > > > > University of Missouri > > > > Columbia, MO 65211 > > > > (573)-823-0616 > > > > cmt...@mi... > > > > > > > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science MU ACM Student Chapter 2005-2006 Program Chair University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
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From: Ed R. <ero...@ug...> - 2005-11-30 15:42:23
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Is there any opposition to my adding the following fields to the SpecialCaseHandler in GUS/Supported for the TranslatedAASequence/Feature methods: source_id, ext_db_rls_id (TranslatedAAFeature,TranslatedAASequence) sequence length (TranslatedAASequence) -ed ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
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From: Michael S. <msa...@pc...> - 2005-11-29 18:26:18
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Sorry. You'll have to back out the previous install before you try again. You can use the dbaDeinstallGus utility to do this (but be careful and read the warnings-- it will delete data). --Mike On Nov 29, 2005, at 1:20 PM, Chris Topinka wrote: > after creating GUS tablespace I get... > > BUILD FAILED > /home/oracle/GUS/project_home/install/build.xml:28: The following > error occurred while executing this line: > /home/oracle/GUS/project_home/GUS/build.xml:92: > java.io.IOException: Error executing SQL: ' > CREATE USER TESSVer IDENTIFIED BY temppass PASSWORD EXPIRE ACCOUNT > LOCK QUOTA UNLIMITED ON USERS DEFAULT TABLESPACE USERS' Error: > ORA-01920: user name 'TESSVER' conflicts with another user or role > name > > > Thanks. > > > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > Hi Chris, > > Ok, you're almost there. Either: > > 1) Create a GUS tablespace > 2) Update your gus_schema.xml file (in $PROJECT_HOME/GusSchema/ > Definition/config) to use tablespace="USERS" (or whatever) instead of > GUS. > > --Mike > > On Nov 29, 2005, at 12:37 PM, Chris Topinka wrote: > > > How should I reply? > > > > Ok. now I get... > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > org.gusdb.schema.InstallSchemaTask execute > > [InstallSchema] INFO: Reading database from /home/oracle/GUS/ > > project_home/GUS/Schema/gus_schema.xml > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > org.gusdb.dbadmin.reader.SchemaReader doRead > > [InstallSchema] INFO: Reading Database > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > org.gusdb.dbadmin.model.Database resolveReferences > > [InstallSchema] INFO: Resolving Database References > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > org.gusdb.dbadmin.util.DatabaseValidator validate > > [InstallSchema] INFO: Validating Database: 'null' > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.schema.InstallSchemaTask setTablespace > > [InstallSchema] INFO: Setting tablespaces to GUS > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.util.DatabaseValidator validate > > [InstallSchema] INFO: Validating Database: 'null' > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.writer.SchemaWriter write > > [InstallSchema] INFO: Writing Database > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.util.DatabaseValidator validate > > [InstallSchema] INFO: Validating Database: 'null' > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.writer.SchemaWriter write > > [InstallSchema] INFO: Writing Database > > > > BUILD FAILED > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > error occurred while executing this line: > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > java.io.IOException : Error executing SQL: ' > > ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: > > tablespace 'GUS' does not exist > > > > > > what is this last line? > > > > On 11/29/05, Michael Saffitz < msa...@pc...> wrote: > > Hi Chris, > > > > Don't use the sys account. Use another account that has been > granted > > dba privileges. > > > > --Mike > > > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > > > when I run build I get... > > > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > > org.gusdb.schema.InstallSchemaTask initialize > > > [InstallSchema] SEVERE: Unable to connect to database. > > > DSN=' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17' > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > sys > > > should be as sysdba or sysoper > > > [InstallSchema] at > > > oracle.jdbc.driver.DatabaseError.throwSqlException > > > (DatabaseError.java:124) > > > [InstallSchema] at > oracle.jdbc.driver.T4CTTIoer.processError > > > (T4CTTIoer.java:304) > > > [InstallSchema] at > oracle.jdbc.driver.T4CTTIoer.processError > > > ( T4CTTIoer.java:271) > > > . > > > . > > > . > > > . > > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > > (Main.java:187) > > > [InstallSchema] at > org.apache.tools.ant.launch.Launcher.run > > > (Launcher.java:246) > > > [InstallSchema] at > org.apache.tools.ant.launch.Launcher.main > > > (Launcher.java:67) > > > > > > BUILD FAILED > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > error occurred while executing this line: > > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect > > > to database > > > > > > Total time: 7 seconds > > > > > > > > > My gus.config looks like this: > > > > > > dbVendor=Oracle > > > dbiDsn=dbi:Oracle: ws17.itcomplab.missouri.edu > > > jdbcDsn=jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17 > > > > > > > > > # Login and Password to the RDBMS > > > > > > databaseLogin=sys > > > databasePassword=adminws17 > > > > > > # Username, group, and project info from the relevant Core tables > > > > > > userName=sys > > > group=sysdba > > > project=Database administration > > > > > > tablespace=GUS > > > > > > Any suggestions? The line: > > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to > sys > > > should be as sysdba or sysoper > > > > > > seems to be the problem. How should I change config? > > > > > > Thanks, > > > > > > chris > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > 113 Life Sciences Center > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... |
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From: Chris T. <cmt...@gm...> - 2005-11-29 18:21:17
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after creating GUS tablespace I get... BUILD FAILED /home/oracle/GUS/project_home/install/build.xml:28: The following error occurred while executing this line: /home/oracle/GUS/project_home/GUS/build.xml:92: java.io.IOException: Error executing SQL: ' CREATE USER TESSVer IDENTIFIED BY temppass PASSWORD EXPIRE ACCOUNT LOCK QUOTA UNLIMITED ON USERS DEFAULT TABLESPACE USERS' Error: ORA-01920: user name 'TESSVER' conflicts with another user or role name Thanks. On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > > Hi Chris, > > Ok, you're almost there. Either: > > 1) Create a GUS tablespace > 2) Update your gus_schema.xml file (in $PROJECT_HOME/GusSchema/ > Definition/config) to use tablespace=3D"USERS" (or whatever) instead of > GUS. > > --Mike > > On Nov 29, 2005, at 12:37 PM, Chris Topinka wrote: > > > How should I reply? > > > > Ok. now I get... > > > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > org.gusdb.schema.InstallSchemaTask execute > > [InstallSchema] INFO: Reading database from /home/oracle/GUS/ > > project_home/GUS/Schema/gus_schema.xml > > [InstallSchema] Nov 29, 2005 11:32:07 AM > > org.gusdb.dbadmin.reader.SchemaReader doRead > > [InstallSchema] INFO: Reading Database > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > org.gusdb.dbadmin.model.Database resolveReferences > > [InstallSchema] INFO: Resolving Database References > > [InstallSchema] Nov 29, 2005 11:32:08 AM > > org.gusdb.dbadmin.util.DatabaseValidator validate > > [InstallSchema] INFO: Validating Database: 'null' > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.schema.InstallSchemaTask setTablespace > > [InstallSchema] INFO: Setting tablespaces to GUS > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.util.DatabaseValidator validate > > [InstallSchema] INFO: Validating Database: 'null' > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.writer.SchemaWriter write > > [InstallSchema] INFO: Writing Database > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.util.DatabaseValidator validate > > [InstallSchema] INFO: Validating Database: 'null' > > [InstallSchema] Nov 29, 2005 11:32:09 AM > > org.gusdb.dbadmin.writer.SchemaWriter write > > [InstallSchema] INFO: Writing Database > > > > BUILD FAILED > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > error occurred while executing this line: > > /home/oracle/GUS/project_home/GUS/build.xml:92: > > java.io.IOException: Error executing SQL: ' > > ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: > > tablespace 'GUS' does not exist > > > > > > what is this last line? > > > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > Hi Chris, > > > > Don't use the sys account. Use another account that has been granted > > dba privileges. > > > > --Mike > > > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > > > when I run build I get... > > > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > > org.gusdb.schema.InstallSchemaTask initialize > > > [InstallSchema] SEVERE: Unable to connect to database. > > > DSN=3D' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521:WS17' > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > > > should be as sysdba or sysoper > > > [InstallSchema] at > > > oracle.jdbc.driver.DatabaseError.throwSqlException > > > (DatabaseError.java:124) > > > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > > > (T4CTTIoer.java:304) > > > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > > > ( T4CTTIoer.java:271) > > > . > > > . > > > . > > > . > > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > > (Main.java:187) > > > [InstallSchema] at org.apache.tools.ant.launch.Launcher.run > > > (Launcher.java:246) > > > [InstallSchema] at org.apache.tools.ant.launch.Launcher.main > > > (Launcher.java:67) > > > > > > BUILD FAILED > > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > > error occurred while executing this line: > > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect > > > to database > > > > > > Total time: 7 seconds > > > > > > > > > My gus.config looks like this: > > > > > > dbVendor=3DOracle > > > dbiDsn=3Ddbi:Oracle:ws17.itcomplab.missouri.edu > > > jdbcDsn=3Djdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17 > > > > > > > > > # Login and Password to the RDBMS > > > > > > databaseLogin=3Dsys > > > databasePassword=3Dadminws17 > > > > > > # Username, group, and project info from the relevant Core tables > > > > > > userName=3Dsys > > > group=3Dsysdba > > > project=3DDatabase administration > > > > > > tablespace=3DGUS > > > > > > Any suggestions? The line: > > > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > > > should be as sysdba or sysoper > > > > > > seems to be the problem. How should I change config? > > > > > > Thanks, > > > > > > chris > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science 113 Life Sciences Center University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
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From: Michael S. <msa...@pc...> - 2005-11-29 17:45:01
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Hi Chris, Ok, you're almost there. Either: 1) Create a GUS tablespace 2) Update your gus_schema.xml file (in $PROJECT_HOME/GusSchema/ Definition/config) to use tablespace="USERS" (or whatever) instead of GUS. --Mike On Nov 29, 2005, at 12:37 PM, Chris Topinka wrote: > How should I reply? > > Ok. now I get... > > [InstallSchema] Nov 29, 2005 11:32:07 AM > org.gusdb.schema.InstallSchemaTask execute > [InstallSchema] INFO: Reading database from /home/oracle/GUS/ > project_home/GUS/Schema/gus_schema.xml > [InstallSchema] Nov 29, 2005 11:32:07 AM > org.gusdb.dbadmin.reader.SchemaReader doRead > [InstallSchema] INFO: Reading Database > [InstallSchema] Nov 29, 2005 11:32:08 AM > org.gusdb.dbadmin.model.Database resolveReferences > [InstallSchema] INFO: Resolving Database References > [InstallSchema] Nov 29, 2005 11:32:08 AM > org.gusdb.dbadmin.util.DatabaseValidator validate > [InstallSchema] INFO: Validating Database: 'null' > [InstallSchema] Nov 29, 2005 11:32:09 AM > org.gusdb.schema.InstallSchemaTask setTablespace > [InstallSchema] INFO: Setting tablespaces to GUS > [InstallSchema] Nov 29, 2005 11:32:09 AM > org.gusdb.dbadmin.util.DatabaseValidator validate > [InstallSchema] INFO: Validating Database: 'null' > [InstallSchema] Nov 29, 2005 11:32:09 AM > org.gusdb.dbadmin.writer.SchemaWriter write > [InstallSchema] INFO: Writing Database > [InstallSchema] Nov 29, 2005 11:32:09 AM > org.gusdb.dbadmin.util.DatabaseValidator validate > [InstallSchema] INFO: Validating Database: 'null' > [InstallSchema] Nov 29, 2005 11:32:09 AM > org.gusdb.dbadmin.writer.SchemaWriter write > [InstallSchema] INFO: Writing Database > > BUILD FAILED > /home/oracle/GUS/project_home/install/build.xml:28: The following > error occurred while executing this line: > /home/oracle/GUS/project_home/GUS/build.xml:92: > java.io.IOException: Error executing SQL: ' > ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: > tablespace 'GUS' does not exist > > > what is this last line? > > On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > Hi Chris, > > Don't use the sys account. Use another account that has been granted > dba privileges. > > --Mike > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > when I run build I get... > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > org.gusdb.schema.InstallSchemaTask initialize > > [InstallSchema] SEVERE: Unable to connect to database. > > DSN=' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521:WS17' > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > > should be as sysdba or sysoper > > [InstallSchema] at > > oracle.jdbc.driver.DatabaseError.throwSqlException > > (DatabaseError.java:124) > > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > > (T4CTTIoer.java:304) > > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > > ( T4CTTIoer.java:271) > > . > > . > > . > > . > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > (Main.java:187) > > [InstallSchema] at org.apache.tools.ant.launch.Launcher.run > > (Launcher.java:246) > > [InstallSchema] at org.apache.tools.ant.launch.Launcher.main > > (Launcher.java:67) > > > > BUILD FAILED > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > error occurred while executing this line: > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect > > to database > > > > Total time: 7 seconds > > > > > > My gus.config looks like this: > > > > dbVendor=Oracle > > dbiDsn=dbi:Oracle:ws17.itcomplab.missouri.edu > > jdbcDsn=jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17 > > > > > > # Login and Password to the RDBMS > > > > databaseLogin=sys > > databasePassword=adminws17 > > > > # Username, group, and project info from the relevant Core tables > > > > userName=sys > > group=sysdba > > project=Database administration > > > > tablespace=GUS > > > > Any suggestions? The line: > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > > should be as sysdba or sysoper > > > > seems to be the problem. How should I change config? > > > > Thanks, > > > > chris > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > 113 Life Sciences Center > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... |
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From: Chris T. <cmt...@gm...> - 2005-11-29 17:37:20
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How should I reply? Ok. now I get... [InstallSchema] Nov 29, 2005 11:32:07 AM org.gusdb.schema.InstallSchemaTaskexecute [InstallSchema] INFO: Reading database from /home/oracle/GUS/project_home/GUS/Schema/gus_schema.xml [InstallSchema] Nov 29, 2005 11:32:07 AM org.gusdb.dbadmin.reader.SchemaReader doRead [InstallSchema] INFO: Reading Database [InstallSchema] Nov 29, 2005 11:32:08 AM org.gusdb.dbadmin.model.DatabaseresolveReferences [InstallSchema] INFO: Resolving Database References [InstallSchema] Nov 29, 2005 11:32:08 AM org.gusdb.dbadmin.util.DatabaseValidator validate [InstallSchema] INFO: Validating Database: 'null' [InstallSchema] Nov 29, 2005 11:32:09 AM org.gusdb.schema.InstallSchemaTasksetTablespace [InstallSchema] INFO: Setting tablespaces to GUS [InstallSchema] Nov 29, 2005 11:32:09 AM org.gusdb.dbadmin.util.DatabaseValidator validate [InstallSchema] INFO: Validating Database: 'null' [InstallSchema] Nov 29, 2005 11:32:09 AM org.gusdb.dbadmin.writer.SchemaWriter write [InstallSchema] INFO: Writing Database [InstallSchema] Nov 29, 2005 11:32:09 AM org.gusdb.dbadmin.util.DatabaseValidator validate [InstallSchema] INFO: Validating Database: 'null' [InstallSchema] Nov 29, 2005 11:32:09 AM org.gusdb.dbadmin.writer.SchemaWriter write [InstallSchema] INFO: Writing Database BUILD FAILED /home/oracle/GUS/project_home/install/build.xml:28: The following error occurred while executing this line: /home/oracle/GUS/project_home/GUS/build.xml:92: java.io.IOException: Error executing SQL: ' ALTER USER SResVer QUOTA UNLIMITED ON GUS' Error: ORA-00959: tablespace 'GUS' does not exist what is this last line? On 11/29/05, Michael Saffitz <msa...@pc...> wrote: > > > Hi Chris, > > Don't use the sys account. Use another account that has been granted > dba privileges. > > --Mike > > On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > > > when I run build I get... > > > > [InstallSchema] Nov 29, 2005 11:12:18 AM > > org.gusdb.schema.InstallSchemaTask initialize > > [InstallSchema] SEVERE: Unable to connect to database. > > DSN=3D'jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521:WS17' > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > > should be as sysdba or sysoper > > [InstallSchema] at > > oracle.jdbc.driver.DatabaseError.throwSqlException > > (DatabaseError.java:124) > > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > > (T4CTTIoer.java:304) > > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > > (T4CTTIoer.java:271) > > . > > . > > . > > . > > [InstallSchema] at org.apache.tools.ant.Main.startAnt > > (Main.java:187) > > [InstallSchema] at org.apache.tools.ant.launch.Launcher.run > > (Launcher.java:246) > > [InstallSchema] at org.apache.tools.ant.launch.Launcher.main > > (Launcher.java:67) > > > > BUILD FAILED > > /home/oracle/GUS/project_home/install/build.xml:28: The following > > error occurred while executing this line: > > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect > > to database > > > > Total time: 7 seconds > > > > > > My gus.config looks like this: > > > > dbVendor=3DOracle > > dbiDsn=3Ddbi:Oracle:ws17.itcomplab.missouri.edu > > jdbcDsn=3Djdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17 > > > > > > # Login and Password to the RDBMS > > > > databaseLogin=3Dsys > > databasePassword=3Dadminws17 > > > > # Username, group, and project info from the relevant Core tables > > > > userName=3Dsys > > group=3Dsysdba > > project=3DDatabase administration > > > > tablespace=3DGUS > > > > Any suggestions? The line: > > > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > > should be as sysdba or sysoper > > > > seems to be the problem. How should I change config? > > > > Thanks, > > > > chris > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science 113 Life Sciences Center University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
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From: Michael S. <msa...@pc...> - 2005-11-29 17:26:41
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Hi Chris, Don't use the sys account. Use another account that has been granted dba privileges. --Mike On Nov 29, 2005, at 12:24 PM, Chris Topinka wrote: > when I run build I get... > > [InstallSchema] Nov 29, 2005 11:12:18 AM > org.gusdb.schema.InstallSchemaTask initialize > [InstallSchema] SEVERE: Unable to connect to database. > DSN='jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521:WS17' > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > should be as sysdba or sysoper > [InstallSchema] at > oracle.jdbc.driver.DatabaseError.throwSqlException > (DatabaseError.java:124) > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > (T4CTTIoer.java:304) > [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError > (T4CTTIoer.java:271) > . > . > . > . > [InstallSchema] at org.apache.tools.ant.Main.startAnt > (Main.java:187) > [InstallSchema] at org.apache.tools.ant.launch.Launcher.run > (Launcher.java:246) > [InstallSchema] at org.apache.tools.ant.launch.Launcher.main > (Launcher.java:67) > > BUILD FAILED > /home/oracle/GUS/project_home/install/build.xml:28: The following > error occurred while executing this line: > /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect > to database > > Total time: 7 seconds > > > My gus.config looks like this: > > dbVendor=Oracle > dbiDsn=dbi:Oracle:ws17.itcomplab.missouri.edu > jdbcDsn=jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521 :WS17 > > > # Login and Password to the RDBMS > > databaseLogin=sys > databasePassword=adminws17 > > # Username, group, and project info from the relevant Core tables > > userName=sys > group=sysdba > project=Database administration > > tablespace=GUS > > Any suggestions? The line: > > [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys > should be as sysdba or sysoper > > seems to be the problem. How should I change config? > > Thanks, > > chris > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > 113 Life Sciences Center > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... |
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From: Chris T. <cmt...@gm...> - 2005-11-29 17:24:32
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when I run build I get... [InstallSchema] Nov 29, 2005 11:12:18 AM org.gusdb.schema.InstallSchemaTaskinitialize [InstallSchema] SEVERE: Unable to connect to database. DSN=3D' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521:WS17' [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys should be as sysdba or sysoper [InstallSchema] at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:124) [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError( T4CTTIoer.java:304) [InstallSchema] at oracle.jdbc.driver.T4CTTIoer.processError( T4CTTIoer.java:271) . . . . [InstallSchema] at org.apache.tools.ant.Main.startAnt(Main.java:187= ) [InstallSchema] at org.apache.tools.ant.launch.Launcher.run( Launcher.java:246) [InstallSchema] at org.apache.tools.ant.launch.Launcher.main( Launcher.java:67) BUILD FAILED /home/oracle/GUS/project_home/install/build.xml:28: The following error occurred while executing this line: /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect to database Total time: 7 seconds My gus.config looks like this: dbVendor=3DOracle dbiDsn=3Ddbi:Oracle:ws17.itcomplab.missouri.edu jdbcDsn=3Djdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521:WS17 # Login and Password to the RDBMS databaseLogin=3Dsys databasePassword=3Dadminws17 # Username, group, and project info from the relevant Core tables userName=3Dsys group=3Dsysdba project=3DDatabase administration tablespace=3DGUS Any suggestions? The line: [InstallSchema] java.sql.SQLException: ORA-28009: connection to sys should be as sysdba or sysoper seems to be the problem. How should I change config? Thanks, chris -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science 113 Life Sciences Center University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
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From: Angel P. <an...@ma...> - 2005-11-28 18:07:12
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Hi all, It was my understanding a while back that GUS was to take an approach that would allow the best of both worlds. Namely, I thought we had agreed to add generic feature and qualifier tables for both NA and AASequences, allowing us to capture arbitrary feature sets while still promoting the "important" features to the named views. Yes, generic views are more chado-like and they pose a threat for over-use and duplication, but in practice I would rather capture all of the features from an external source and possibly duplicate some features than miss some. This sort of situation would arise, for example, when subsequent releases of the DB are loaded after a feature gets "promoted" As for whole sequence attributes, are either of these acceptable solutions? a) leaving locations blank b) creating a location that spans the entire sequence for sequence attributes If not, I don't mind a generic sequence attribute table. -Angel Chris Stoeckert wrote: > Hi Aaron, > see comments in line. > > On Nov 22, 2005, at 4:03 PM, am...@pc... wrote: > >> Quoting Chris Stoeckert <sto...@pc...>: >> >>> if these are overlooked attributes that really should be part of >>> any sequence then we would alter the base NASequence/ AASequence >>> tables. >> >> >> Some are, some aren't. The most notable ones to be included in base >> AASequence >> are min_molecular_weight and max_molecular_weight (just as you >> already use >> min_start and max_start to handle fuzzy locations). >> isoelectric_point also >> seems like a "should have". >> >> But "hydropathicity_gravy_score" and "aromaticity_score" are just >> the tip of a >> long list of esoteric attributes that creating a two-column view called >> DoTS.AASequenceAromaticity (aa_sequence_id, aromaticity_score) seems >> like >> overkill, and would lead to further proliferation of the schema. >> >>> The major argument I would see for weak typed tag values is that >>> there is a long and arbitrary list of such attributes but I'm not >>> convinced that this is the case. >> >> >> You're not convinced because you haven't seen a long and arbitrary >> list, or >> because you don't believe one could actually exist? > > > Both. And I should clarify that this applies to what groups would > commonly store not what you (or anyone) can imagine (i.e., capture > practical requirements) . This may reflect my ignorance of > "hydropathicity_gravy_score" and am happy to be enlightened about > why that is practically needed in the core GUS schema. Note of course > that any group can of course add whatever special attributes to their > GUS instance; it is where multiple groups need the same attributes > that we want to capture this in core GUS. The downside to a weakly > typed attribute table is the potential to have multiple entries for > the same thing unless a controlled vocabulary can be used. > >> On a related topic, how should we handle organellar/compartmental >> targetting >> predictions (i.e. not signalP predictions that are easily handled as >> locatable >> features, but rather output from such things as MitoPred and TargetP >> that again >> provide non-locatable "attributes" to an AASequence). One route >> would be to >> associate the GO component term via an IEA evidence code - but then >> where do >> the algorithm_id and score(s) go? Alternatively, these become yet more >> AASequence attributes ... > > > Actually, these are easily captured as AAFeatures which has a foreign > key to AASequence. Locatable features are specified with AALocation > with a foreign key to AAFeature. In fact, one can use > PredictedAAFeature. > > This does underscore a semantic distinction between predicted > features and sequence attributes. Attributes can be anything of > course, and as such has no constraint on what is put there (including > things that should be put elsewhere). > > Cheers, > Chris > >> Thanks, >> >> -Aaron >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by the JBoss Inc. Get Certified Today >> Register for a JBoss Training Course. Free Certification Exam >> for All Training Attendees Through End of 2005. For more info visit: >> http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 |
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From: Josef J. <ju...@cs...> - 2005-11-28 17:48:07
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Chris Stoeckert <sto...@pc...> writes: > > The unique constraint on source_id of AAEntry/NAEntry will be > eliminated in the next release. To help me remember, please enter a > bug request. Will do; > Thanks for bringing this up. And thank you for taking a look; Also, something you might want to consider is putting the fields of AAEntry/NAEntry into ExternalAASequence/ExternalNASequence and then eliminating AAEntry/NAEntry. As the ExternalAASequence/ExternalNASequence views are intended to hold information on public sequences such as those from genbank/swissprot records, then there is no reason to keep the dates of these records in a separate table. I was actually struggling with finding an elegant way of putting swissprot sequence dates into ExternalAASequence until I stumbled upon AAEntry. I can see no reason why the dates of these records should be in a separate table, and actually simplifying the schema without loosing any functionality would be a big plus. Thanks, Josef |
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From: Chris S. <sto...@pc...> - 2005-11-28 12:53:35
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Hi Josef, The unique constraint on source_id of AAEntry/NAEntry will be eliminated in the next release. To help me remember, please enter a bug request. Thanks for bringing this up. Cheers, Chris On Nov 16, 2005, at 3:53 PM, Josef Jurek wrote: > > Deborah Pinney <pi...@pc...> writes: >> >> There is a case here at Cbil, where we need to have the constraint in >> place. In that case dots.naentry is used as a book-keeping tool to >> keep >> track of modifications of Genbank entries. > > This should be the purpose of the *_DATE and *_REL_VER fields, > to keep track of the modification of genbank entries. > Why would you need anything else? > > This unique constraint sounds like it was implemented for > idiosyncratic reasons by someone at CBIL. I'll bet this field > will continue to completely serve your needs if the unique > constraint is removed. > > That the source_id field is provided in many tables to give > users at their respective sites the ability to do local > bookkeeping is great. Putting a unique constraint > on this field for a perceived local bookkeeping need > is just a stumbling block that adds a bit of difficulty > to the GUS community. > > > So, shall this unique constraint on source_id of > AAEntry/NAEntry be eliminated? (We don't have to > decide today). > > Thanks for the response; Josef > > > >> I think at one time the >> constraint did not apply to dots.aaentry.source_id (I can't swear on >> that though). That may have changed for the sake of consistency. >> >> Josef Jurek wrote: >> >>> Well, if people do not feel that source_id requires >>> an unique constraint in tables AAEntry/NAEntry, >>> I propose that these constraints be removed. I can >>> of course just remove them in our local gus installations, >>> though I would prefer that our local development >>> of tools be compatible with canonical GUS. >>> >> >> Another option would be to just include the fields: >> >> CREATED_DATE DATE >> CREATED_REL_VER NUMBER(5) >> SEQ_DATE DATE >> SEQ_REL_VER NUMBER(5) >> ANNOT_DATE DATE >> ANNOT_REL_VER NUMBER(5) >> >> into AASequenceImp/NASequenceImp and eliminate > [...] > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Chris S. <sto...@pc...> - 2005-11-27 23:31:49
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Hi Aaron, see comments in line. On Nov 22, 2005, at 4:03 PM, am...@pc... wrote: > Quoting Chris Stoeckert <sto...@pc...>: > >> if these are overlooked attributes that really should be part of >> any sequence then we would alter the base NASequence/ AASequence >> tables. > > Some are, some aren't. The most notable ones to be included in > base AASequence > are min_molecular_weight and max_molecular_weight (just as you > already use > min_start and max_start to handle fuzzy locations). > isoelectric_point also > seems like a "should have". > > But "hydropathicity_gravy_score" and "aromaticity_score" are just > the tip of a > long list of esoteric attributes that creating a two-column view > called > DoTS.AASequenceAromaticity (aa_sequence_id, aromaticity_score) > seems like > overkill, and would lead to further proliferation of the schema. > >> The major argument I would see for weak typed tag values is that >> there is a long and arbitrary list of such attributes but I'm not >> convinced that this is the case. > > You're not convinced because you haven't seen a long and arbitrary > list, or > because you don't believe one could actually exist? Both. And I should clarify that this applies to what groups would commonly store not what you (or anyone) can imagine (i.e., capture practical requirements) . This may reflect my ignorance of "hydropathicity_gravy_score" and am happy to be enlightened about why that is practically needed in the core GUS schema. Note of course that any group can of course add whatever special attributes to their GUS instance; it is where multiple groups need the same attributes that we want to capture this in core GUS. The downside to a weakly typed attribute table is the potential to have multiple entries for the same thing unless a controlled vocabulary can be used. > On a related topic, how should we handle organellar/compartmental > targetting > predictions (i.e. not signalP predictions that are easily handled > as locatable > features, but rather output from such things as MitoPred and > TargetP that again > provide non-locatable "attributes" to an AASequence). One route > would be to > associate the GO component term via an IEA evidence code - but then > where do > the algorithm_id and score(s) go? Alternatively, these become yet > more > AASequence attributes ... Actually, these are easily captured as AAFeatures which has a foreign key to AASequence. Locatable features are specified with AALocation with a foreign key to AAFeature. In fact, one can use PredictedAAFeature. This does underscore a semantic distinction between predicted features and sequence attributes. Attributes can be anything of course, and as such has no constraint on what is put there (including things that should be put elsewhere). Cheers, Chris > Thanks, > > -Aaron > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Ed R. <ero...@ug...> - 2005-11-23 22:41:32
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We are still using an old plugin in GUS 3.0 to support some work some graduate students are doing with Trypanosome data. The data involves TIGR XML files for T.cruzi, T.brucei and L.major. Unfortunately, one of the T.brucei files is not loading. A dump of the data shows that complex features with many exons are incorrectly being added as hashrefs to the object hierarchy and this causes a failure once the object tree is submitted. If this sounds vaguely familiar to anyone on this list, please let us know. I will post a more detailed description including error messages once I am at a location where I can open a telnet session back to our lab. -Ed Robinson |
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From: <am...@pc...> - 2005-11-22 21:03:46
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Quoting Chris Stoeckert <sto...@pc...>: > if these are overlooked attributes that really should be part of any > sequence then we would alter the base NASequence/ AASequence tables. Some are, some aren't. The most notable ones to be included in base AASequence are min_molecular_weight and max_molecular_weight (just as you already use min_start and max_start to handle fuzzy locations). isoelectric_point also seems like a "should have". But "hydropathicity_gravy_score" and "aromaticity_score" are just the tip of a long list of esoteric attributes that creating a two-column view called DoTS.AASequenceAromaticity (aa_sequence_id, aromaticity_score) seems like overkill, and would lead to further proliferation of the schema. > The major argument I would see for weak typed tag values is that > there is a long and arbitrary list of such attributes but I'm not > convinced that this is the case. You're not convinced because you haven't seen a long and arbitrary list, or because you don't believe one could actually exist? On a related topic, how should we handle organellar/compartmental targetting predictions (i.e. not signalP predictions that are easily handled as locatable features, but rather output from such things as MitoPred and TargetP that again provide non-locatable "attributes" to an AASequence). One route would be to associate the GO component term via an IEA evidence code - but then where do the algorithm_id and score(s) go? Alternatively, these become yet more AASequence attributes ... Thanks, -Aaron |
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From: Jian Lu <jl...@vb...> - 2005-11-22 18:59:10
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Hi Folks, The current gene ontology plugin (GUS::Supported::Plugin::InsertGeneOntology) can only insert new GO terms into a database. In order to update GO terms, each time we have to delete old ones and do fresh insertion. However if there is any association with GO terms, what should we do? Reload everything? Is there any other option? Thanks. Happy Thanksgiving! Jian |
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