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From: Steve F. <sfi...@pc...> - 2004-06-09 21:00:50
|
michael-
it looks like you added a row to TableInfo for the
SResVer::MassSpecSummary. if so, delete it and build again.
steve
Michael Luchtan wrote:
>It has been a long time since a build took place here, and I was not
>really present for the installation of GUS. But in the checkouts
>directory I checked out GUS from Sanger. I executed the
>build GUS install -append
>and got the following errors:
> [exec] generating java object for SResVer::MassSpecSummary
> [exec] Error: Package Table Name '' is not in the form of
>org.gusdb.model.SCHEMA.NAME at /var/lo\
>cal/gus_home/lib/perl/GUS/ObjRelP/Generator/RowGenerator.pm line 91
> [exec]
>GUS::ObjRelP::Generator::RowGenerator::_cutPackageTableName('GUS::ObjRelP::Generator::\
>JavaRowGenerator=HASH(0x83955d0)', undef) called at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator\
>/JavaRowGenerator.pm line 410
> [exec]
>GUS::ObjRelP::Generator::JavaRowGenerator::_createParentAccessors('GUS::ObjRelP::Gener\
>ator::JavaRowGenerator=HASH(0x83955d0)', 'HASH(0x85d48ec)') called at
>/var/local/gus_home/lib/perl/GUS\
>/ObjRelP/Generator/JavaRowGenerator.pm line 127
> [exec]
>GUS::ObjRelP::Generator::JavaRowGenerator::_genAccessors('GUS::ObjRelP::Generator::Jav\
>aRowGenerator=HASH(0x83955d0)') called at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/JavaRowGe\
>nerator.pm line 32
> [exec]
>GUS::ObjRelP::Generator::JavaRowGenerator::generate('GUS::ObjRelP::Generator::JavaRowG\
>enerator=HASH(0x83955d0)', undef) called at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/Generat\
>or.pm line 109
> [exec]
>GUS::ObjRelP::Generator::Generator::generate('GUS::ObjRelP::Generator::Generator=HASH(\
>0x81073d4)', undef) called at /var/local/gus_home/bin/generateGusObjects
>line 67
>
>BUILD FAILED
>file:/var/local/checkout/GUS/build.xml:114: exec returned: -1
>
>
>According to the VBI install docs, it is necessary to edit the build.xml
>and take out the generateGusObjects executable statement first. But
>after this I get the following errors:
> [echo] Installing GUS/Model
> [javac] Compiling 5 source files to
>/var/local/checkout/GUS/Model/classes
> [javac]
>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/MassSpecSummary_Table.java:\
>17: illegal start of expression
> [javac] tableAtts.put("", new GUSTableAttribute("", "",
>"java.lang.notdefyet", -1, , -1, f\
>alse, false) );
>
>[javac] ^
> [javac]
>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/MassSpecSummary_Table.java:\
>17: ')' expected
> [javac] tableAtts.put("", new GUSTableAttribute("", "",
>"java.lang.notdefyet", -1, , -1, f\
>alse, false) );
>
>[javac] \
> ^
> [javac] 2 errors
>
>BUILD FAILED
>file:/var/local/checkout/install/build.xml:227: Compile failed; see the
>compiler error output for deta\
>ils.
>
>
>Any help is appreciated....
>Michael Luchtan
>
>
>
>
>
>On Wed, 2004-06-09 at 16:10, Steve Fischer wrote:
>
>
>>michael-
>>
>>we have seen this. i think if you get the latest from cvs and then
>>rebuild the objects you will get around this problem.
>>
>>then, use submitrow to add rows to tableinfo for the mass spec tables
>>and rebuild all over again.
>>
>>steve
>>
>>Michael Luchtan wrote:
>>
>>
>>
>>>Hello--
>>>Can you give me a heads up on why I cannot use the submitrow plugin any
>>>more, now that I have rebuild the perl object layer? Hope I didn't just
>>>screw myself...
>>>
>>>Here is the command/arguement:
>>>
>>>luchtan]# ga GUS::Common::Plugin::SubmitRow --tablename Core::UserInfo
>>>--attrlist
>>>"login,password,first_name,last_name,e_mail,modification_date"
>>>--valuelist
>>>"pablo^^^pablo123^^^pablo^^^mendes^^^pa...@pa...^^^SYSDATE"
>>>Reading properties from /var/local/gus_home/config/GUS-PluginMgr.prop
>>>Reading properties from /home/luchtan/.gus.properties
>>>DBD::Oracle::st execute failed: ORA-00001: unique constraint
>>>(CORE.PK_ALGORITHMINVOCATION) violated (DBD ERROR: OCIStmtExecute) at
>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
>>>
>>>SQL ERROR!! involving
>>>
>>> INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_id,
>>>user_write, group_write, cpu_time, algorithm_implementation_id,
>>>row_project_id, algorithm_invocation_id, comment_string, group_read,
>>>row_group_id, result, other_read, cpus_used, start_time,
>>>modification_date, user_read, row_alg_invocation_id, other_write,
>>>machine_id )
>>> VALUES ( SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?,
>>>SYSDATE, SYSDATE, ?, ?, ?, ? )
>>>Values: 4, 1, 1, 0, 3, 2, 25, 1, 2, pending, 1, 1, 1, 1, 0, 0 at
>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>>>
>>>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', '^J SQL ERROR!! involving^J ^J INSERT INTO Core.AlgorithmInvocati...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>>>
>>>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x873690c)', 'ARRAY(0x87377c4)', '^J INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
>>>
>>>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)', 'HASH(0x86a9574)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621
>>>
>>>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>>>
>>>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 939
>>>
>>>GUS::PluginMgr::GusApplication::openInvocation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow=HASH(0x850872c)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 425
>>>
>>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>>>
>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>>>
>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
>>>Issuing rollback() for database handle being DESTROY'd without explicit
>>>disconnect().
>>>
>>>
>>>On Wed, 2004-06-09 at 14:52, Steve Fischer wrote:
>>>
>>>
>>>
>>>
>>>>I have added instructions for this to the wiki. see if you can find it.
>>>>
>>>>steve
>>>>
>>>>Michael Luchtan wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Hello-
>>>>>We are attempting to load some mass spec data into gus. Well, the
>>>>>version of gus that we have did not contain two of the relevant tables:
>>>>>DoTS.MassSpecFeature and DoTS.MassSpecSummary
>>>>>I created the MassSpecFeature view on DoTS.aafeatureimp and the table
>>>>>dots.massspecsummary.
>>>>>Now we need to generate the GUS objects for the tables for use in
>>>>>plug-ins. All of the oerl modules in GUS/Model/* are generated
>>>>>automagically. It looks like I could just copy some files and change
>>>>>the names. But they all say something like this:
>>>>>
>>>>># THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE
>>>>>GUS::ObjRelP::Generator
>>>>># PACKAGE.
>>>>>#
>>>>># DO NOT EDIT!!
>>>>>
>>>>># TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO
>>>>>InteractionType.pm.man
>>>>># (or edit that file if it already exists) AND ADD THE FUNCTIONALITY
>>>>>THERE.
>>>>># THEN RE-GENERATE THE GUS OBJECTS.
>>>>>
>>>>>Any word on how to use the Generator? Any help is appreciated. It
>>>>>might go well in the Wiki-wiki!
>>>>>
>>>>>Michael Luchtan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>-------------------------------------------------------
>>>>>This SF.Net email is sponsored by: GNOME Foundation
>>>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
>>>>>GNOME Users and Developers European Conference, 28-30th June in Norway
>>>>>http://2004/guadec.org
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by: GNOME Foundation
>>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
>>>>GNOME Users and Developers European Conference, 28-30th June in Norway
>>>>http://2004/guadec.org
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by: GNOME Foundation
>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
>>>GNOME Users and Developers European Conference, 28-30th June in Norway
>>>http://2004/guadec.org
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>>
|
|
From: Michael L. <lu...@ug...> - 2004-06-09 20:46:09
|
It has been a long time since a build took place here, and I was not
really present for the installation of GUS. But in the checkouts
directory I checked out GUS from Sanger. I executed the
build GUS install -append
and got the following errors:
[exec] generating java object for SResVer::MassSpecSummary
[exec] Error: Package Table Name '' is not in the form of
org.gusdb.model.SCHEMA.NAME at /var/lo\
cal/gus_home/lib/perl/GUS/ObjRelP/Generator/RowGenerator.pm line 91
[exec]
GUS::ObjRelP::Generator::RowGenerator::_cutPackageTableName('GUS::ObjRelP::Generator::\
JavaRowGenerator=HASH(0x83955d0)', undef) called at
/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator\
/JavaRowGenerator.pm line 410
[exec]
GUS::ObjRelP::Generator::JavaRowGenerator::_createParentAccessors('GUS::ObjRelP::Gener\
ator::JavaRowGenerator=HASH(0x83955d0)', 'HASH(0x85d48ec)') called at
/var/local/gus_home/lib/perl/GUS\
/ObjRelP/Generator/JavaRowGenerator.pm line 127
[exec]
GUS::ObjRelP::Generator::JavaRowGenerator::_genAccessors('GUS::ObjRelP::Generator::Jav\
aRowGenerator=HASH(0x83955d0)') called at
/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/JavaRowGe\
nerator.pm line 32
[exec]
GUS::ObjRelP::Generator::JavaRowGenerator::generate('GUS::ObjRelP::Generator::JavaRowG\
enerator=HASH(0x83955d0)', undef) called at
/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/Generat\
or.pm line 109
[exec]
GUS::ObjRelP::Generator::Generator::generate('GUS::ObjRelP::Generator::Generator=HASH(\
0x81073d4)', undef) called at /var/local/gus_home/bin/generateGusObjects
line 67
BUILD FAILED
file:/var/local/checkout/GUS/build.xml:114: exec returned: -1
According to the VBI install docs, it is necessary to edit the build.xml
and take out the generateGusObjects executable statement first. But
after this I get the following errors:
[echo] Installing GUS/Model
[javac] Compiling 5 source files to
/var/local/checkout/GUS/Model/classes
[javac]
/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/MassSpecSummary_Table.java:\
17: illegal start of expression
[javac] tableAtts.put("", new GUSTableAttribute("", "",
"java.lang.notdefyet", -1, , -1, f\
alse, false) );
[javac] ^
[javac]
/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/MassSpecSummary_Table.java:\
17: ')' expected
[javac] tableAtts.put("", new GUSTableAttribute("", "",
"java.lang.notdefyet", -1, , -1, f\
alse, false) );
[javac] \
^
[javac] 2 errors
BUILD FAILED
file:/var/local/checkout/install/build.xml:227: Compile failed; see the
compiler error output for deta\
ils.
Any help is appreciated....
Michael Luchtan
On Wed, 2004-06-09 at 16:10, Steve Fischer wrote:
> michael-
>
> we have seen this. i think if you get the latest from cvs and then
> rebuild the objects you will get around this problem.
>
> then, use submitrow to add rows to tableinfo for the mass spec tables
> and rebuild all over again.
>
> steve
>
> Michael Luchtan wrote:
>
> >Hello--
> >Can you give me a heads up on why I cannot use the submitrow plugin any
> >more, now that I have rebuild the perl object layer? Hope I didn't just
> >screw myself...
> >
> >Here is the command/arguement:
> >
> > luchtan]# ga GUS::Common::Plugin::SubmitRow --tablename Core::UserInfo
> >--attrlist
> >"login,password,first_name,last_name,e_mail,modification_date"
> >--valuelist
> >"pablo^^^pablo123^^^pablo^^^mendes^^^pa...@pa...^^^SYSDATE"
> >Reading properties from /var/local/gus_home/config/GUS-PluginMgr.prop
> >Reading properties from /home/luchtan/.gus.properties
> >DBD::Oracle::st execute failed: ORA-00001: unique constraint
> >(CORE.PK_ALGORITHMINVOCATION) violated (DBD ERROR: OCIStmtExecute) at
> >/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
> >
> > SQL ERROR!! involving
> >
> > INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_id,
> >user_write, group_write, cpu_time, algorithm_implementation_id,
> >row_project_id, algorithm_invocation_id, comment_string, group_read,
> >row_group_id, result, other_read, cpus_used, start_time,
> >modification_date, user_read, row_alg_invocation_id, other_write,
> >machine_id )
> > VALUES ( SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?,
> >SYSDATE, SYSDATE, ?, ?, ?, ? )
> > Values: 4, 1, 1, 0, 3, 2, 25, 1, 2, pending, 1, 1, 1, 1, 0, 0 at
> >/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
> >
> >GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', '^J SQL ERROR!! involving^J ^J INSERT INTO Core.AlgorithmInvocati...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
> >
> >GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x873690c)', 'ARRAY(0x87377c4)', '^J INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> >
> >GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)', 'HASH(0x86a9574)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621
> >
> >GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >
> >GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 939
> >
> >GUS::PluginMgr::GusApplication::openInvocation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow=HASH(0x850872c)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 425
> >
> >GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
> >
> >GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
> >
> >GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
> >Issuing rollback() for database handle being DESTROY'd without explicit
> >disconnect().
> >
> >
> >On Wed, 2004-06-09 at 14:52, Steve Fischer wrote:
> >
> >
> >>I have added instructions for this to the wiki. see if you can find it.
> >>
> >>steve
> >>
> >>Michael Luchtan wrote:
> >>
> >>
> >>
> >>>Hello-
> >>>We are attempting to load some mass spec data into gus. Well, the
> >>>version of gus that we have did not contain two of the relevant tables:
> >>>DoTS.MassSpecFeature and DoTS.MassSpecSummary
> >>>I created the MassSpecFeature view on DoTS.aafeatureimp and the table
> >>>dots.massspecsummary.
> >>>Now we need to generate the GUS objects for the tables for use in
> >>>plug-ins. All of the oerl modules in GUS/Model/* are generated
> >>>automagically. It looks like I could just copy some files and change
> >>>the names. But they all say something like this:
> >>>
> >>># THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE
> >>>GUS::ObjRelP::Generator
> >>># PACKAGE.
> >>>#
> >>># DO NOT EDIT!!
> >>>
> >>># TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO
> >>>InteractionType.pm.man
> >>># (or edit that file if it already exists) AND ADD THE FUNCTIONALITY
> >>>THERE.
> >>># THEN RE-GENERATE THE GUS OBJECTS.
> >>>
> >>>Any word on how to use the Generator? Any help is appreciated. It
> >>>might go well in the Wiki-wiki!
> >>>
> >>>Michael Luchtan
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.Net email is sponsored by: GNOME Foundation
> >>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
> >>>GNOME Users and Developers European Conference, 28-30th June in Norway
> >>>http://2004/guadec.org
> >>>_______________________________________________
> >>>Gusdev-gusdev mailing list
> >>>Gus...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>
> >>>
> >>>
> >>>
> >>
> >>-------------------------------------------------------
> >>This SF.Net email is sponsored by: GNOME Foundation
> >>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
> >>GNOME Users and Developers European Conference, 28-30th June in Norway
> >>http://2004/guadec.org
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: GNOME Foundation
> >Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
> >GNOME Users and Developers European Conference, 28-30th June in Norway
> >http://2004/guadec.org
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
|
|
From: Steve F. <sfi...@pc...> - 2004-06-09 20:10:33
|
michael-
we have seen this. i think if you get the latest from cvs and then
rebuild the objects you will get around this problem.
then, use submitrow to add rows to tableinfo for the mass spec tables
and rebuild all over again.
steve
Michael Luchtan wrote:
>Hello--
>Can you give me a heads up on why I cannot use the submitrow plugin any
>more, now that I have rebuild the perl object layer? Hope I didn't just
>screw myself...
>
>Here is the command/arguement:
>
> luchtan]# ga GUS::Common::Plugin::SubmitRow --tablename Core::UserInfo
>--attrlist
>"login,password,first_name,last_name,e_mail,modification_date"
>--valuelist
>"pablo^^^pablo123^^^pablo^^^mendes^^^pa...@pa...^^^SYSDATE"
>Reading properties from /var/local/gus_home/config/GUS-PluginMgr.prop
>Reading properties from /home/luchtan/.gus.properties
>DBD::Oracle::st execute failed: ORA-00001: unique constraint
>(CORE.PK_ALGORITHMINVOCATION) violated (DBD ERROR: OCIStmtExecute) at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
>
> SQL ERROR!! involving
>
> INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_id,
>user_write, group_write, cpu_time, algorithm_implementation_id,
>row_project_id, algorithm_invocation_id, comment_string, group_read,
>row_group_id, result, other_read, cpus_used, start_time,
>modification_date, user_read, row_alg_invocation_id, other_write,
>machine_id )
> VALUES ( SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?,
>SYSDATE, SYSDATE, ?, ?, ?, ? )
> Values: 4, 1, 1, 0, 3, 2, 25, 1, 2, pending, 1, 1, 1, 1, 0, 0 at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>
>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', '^J SQL ERROR!! involving^J ^J INSERT INTO Core.AlgorithmInvocati...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>
>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x873690c)', 'ARRAY(0x87377c4)', '^J INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
>
>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)', 'HASH(0x86a9574)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621
>
>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>
>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 939
>
>GUS::PluginMgr::GusApplication::openInvocation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow=HASH(0x850872c)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 425
>
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
>Issuing rollback() for database handle being DESTROY'd without explicit
>disconnect().
>
>
>On Wed, 2004-06-09 at 14:52, Steve Fischer wrote:
>
>
>>I have added instructions for this to the wiki. see if you can find it.
>>
>>steve
>>
>>Michael Luchtan wrote:
>>
>>
>>
>>>Hello-
>>>We are attempting to load some mass spec data into gus. Well, the
>>>version of gus that we have did not contain two of the relevant tables:
>>>DoTS.MassSpecFeature and DoTS.MassSpecSummary
>>>I created the MassSpecFeature view on DoTS.aafeatureimp and the table
>>>dots.massspecsummary.
>>>Now we need to generate the GUS objects for the tables for use in
>>>plug-ins. All of the oerl modules in GUS/Model/* are generated
>>>automagically. It looks like I could just copy some files and change
>>>the names. But they all say something like this:
>>>
>>># THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE
>>>GUS::ObjRelP::Generator
>>># PACKAGE.
>>>#
>>># DO NOT EDIT!!
>>>
>>># TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO
>>>InteractionType.pm.man
>>># (or edit that file if it already exists) AND ADD THE FUNCTIONALITY
>>>THERE.
>>># THEN RE-GENERATE THE GUS OBJECTS.
>>>
>>>Any word on how to use the Generator? Any help is appreciated. It
>>>might go well in the Wiki-wiki!
>>>
>>>Michael Luchtan
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by: GNOME Foundation
>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
>>>GNOME Users and Developers European Conference, 28-30th June in Norway
>>>http://2004/guadec.org
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by: GNOME Foundation
>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
>>GNOME Users and Developers European Conference, 28-30th June in Norway
>>http://2004/guadec.org
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: GNOME Foundation
>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
>GNOME Users and Developers European Conference, 28-30th June in Norway
>http://2004/guadec.org
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
|
|
From: Angel P. <an...@pc...> - 2004-06-09 19:31:33
|
Michael Luchtan wrote: >Steve, >Easy to find on the Wiki-wiki. Seems like it remade the perl object >layer, but still no massspec objects. Any other ideas? > >VERSION >is just a file that says 3.0 > > >If anyone wants, they could just include send us these files: >GUS::Model::DoTS::Mass* > > > It is very important that you add the new views to Core.TableInfo, since that is the table that the object generator uses to make the objects. Make entries for DoTS::MAss* in tableinfo and regenerate the objects Angel |
|
From: Michael L. <lu...@ug...> - 2004-06-09 19:30:59
|
Hello--
Can you give me a heads up on why I cannot use the submitrow plugin any
more, now that I have rebuild the perl object layer? Hope I didn't just
screw myself...
Here is the command/arguement:
luchtan]# ga GUS::Common::Plugin::SubmitRow --tablename Core::UserInfo
--attrlist
"login,password,first_name,last_name,e_mail,modification_date"
--valuelist
"pablo^^^pablo123^^^pablo^^^mendes^^^pa...@pa...^^^SYSDATE"
Reading properties from /var/local/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(CORE.PK_ALGORITHMINVOCATION) violated (DBD ERROR: OCIStmtExecute) at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
SQL ERROR!! involving
INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_id,
user_write, group_write, cpu_time, algorithm_implementation_id,
row_project_id, algorithm_invocation_id, comment_string, group_read,
row_group_id, result, other_read, cpus_used, start_time,
modification_date, user_read, row_alg_invocation_id, other_write,
machine_id )
VALUES ( SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?,
SYSDATE, SYSDATE, ?, ?, ?, ? )
Values: 4, 1, 1, 0, 3, 2, 25, 1, 2, pending, 1, 1, 1, 1, 0, 0 at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', '^J SQL ERROR!! involving^J ^J INSERT INTO Core.AlgorithmInvocati...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x873690c)', 'ARRAY(0x87377c4)', '^J INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)', 'HASH(0x86a9574)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621
GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 939
GUS::PluginMgr::GusApplication::openInvocation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow=HASH(0x850872c)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 425
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
Issuing rollback() for database handle being DESTROY'd without explicit
disconnect().
On Wed, 2004-06-09 at 14:52, Steve Fischer wrote:
> I have added instructions for this to the wiki. see if you can find it.
>
> steve
>
> Michael Luchtan wrote:
>
> >Hello-
> >We are attempting to load some mass spec data into gus. Well, the
> >version of gus that we have did not contain two of the relevant tables:
> >DoTS.MassSpecFeature and DoTS.MassSpecSummary
> >I created the MassSpecFeature view on DoTS.aafeatureimp and the table
> >dots.massspecsummary.
> >Now we need to generate the GUS objects for the tables for use in
> >plug-ins. All of the oerl modules in GUS/Model/* are generated
> >automagically. It looks like I could just copy some files and change
> >the names. But they all say something like this:
> >
> ># THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE
> >GUS::ObjRelP::Generator
> ># PACKAGE.
> >#
> ># DO NOT EDIT!!
> >
> ># TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO
> >InteractionType.pm.man
> ># (or edit that file if it already exists) AND ADD THE FUNCTIONALITY
> >THERE.
> ># THEN RE-GENERATE THE GUS OBJECTS.
> >
> >Any word on how to use the Generator? Any help is appreciated. It
> >might go well in the Wiki-wiki!
> >
> >Michael Luchtan
> >
> >
> >
> >
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: GNOME Foundation
> >Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
> >GNOME Users and Developers European Conference, 28-30th June in Norway
> >http://2004/guadec.org
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: GNOME Foundation
> Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
> GNOME Users and Developers European Conference, 28-30th June in Norway
> http://2004/guadec.org
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
|
|
From: Michael L. <lu...@ug...> - 2004-06-09 19:13:46
|
Steve, Easy to find on the Wiki-wiki. Seems like it remade the perl object layer, but still no massspec objects. Any other ideas? VERSION is just a file that says 3.0 If anyone wants, they could just include send us these files: GUS::Model::DoTS::Mass* Michael Luchtan On Wed, 2004-06-09 at 14:52, Steve Fischer wrote: > I have added instructions for this to the wiki. see if you can find it. > > steve > > Michael Luchtan wrote: > > >Hello- > >We are attempting to load some mass spec data into gus. Well, the > >version of gus that we have did not contain two of the relevant tables: > >DoTS.MassSpecFeature and DoTS.MassSpecSummary > >I created the MassSpecFeature view on DoTS.aafeatureimp and the table > >dots.massspecsummary. > >Now we need to generate the GUS objects for the tables for use in > >plug-ins. All of the oerl modules in GUS/Model/* are generated > >automagically. It looks like I could just copy some files and change > >the names. But they all say something like this: > > > ># THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE > >GUS::ObjRelP::Generator > ># PACKAGE. > ># > ># DO NOT EDIT!! > > > ># TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO > >InteractionType.pm.man > ># (or edit that file if it already exists) AND ADD THE FUNCTIONALITY > >THERE. > ># THEN RE-GENERATE THE GUS OBJECTS. > > > >Any word on how to use the Generator? Any help is appreciated. It > >might go well in the Wiki-wiki! > > > >Michael Luchtan > > > > > > > > > > > > > > > > > >------------------------------------------------------- > >This SF.Net email is sponsored by: GNOME Foundation > >Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > >GNOME Users and Developers European Conference, 28-30th June in Norway > >http://2004/guadec.org > >_______________________________________________ > >Gusdev-gusdev mailing list > >Gus...@li... > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: GNOME Foundation > Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > GNOME Users and Developers European Conference, 28-30th June in Norway > http://2004/guadec.org > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Steve F. <sfi...@pc...> - 2004-06-09 18:52:38
|
I have added instructions for this to the wiki. see if you can find it. steve Michael Luchtan wrote: >Hello- >We are attempting to load some mass spec data into gus. Well, the >version of gus that we have did not contain two of the relevant tables: >DoTS.MassSpecFeature and DoTS.MassSpecSummary >I created the MassSpecFeature view on DoTS.aafeatureimp and the table >dots.massspecsummary. >Now we need to generate the GUS objects for the tables for use in >plug-ins. All of the oerl modules in GUS/Model/* are generated >automagically. It looks like I could just copy some files and change >the names. But they all say something like this: > ># THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE >GUS::ObjRelP::Generator ># PACKAGE. ># ># DO NOT EDIT!! > ># TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO >InteractionType.pm.man ># (or edit that file if it already exists) AND ADD THE FUNCTIONALITY >THERE. ># THEN RE-GENERATE THE GUS OBJECTS. > >Any word on how to use the Generator? Any help is appreciated. It >might go well in the Wiki-wiki! > >Michael Luchtan > > > > > > > > >------------------------------------------------------- >This SF.Net email is sponsored by: GNOME Foundation >Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. >GNOME Users and Developers European Conference, 28-30th June in Norway >http://2004/guadec.org >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Michael L. <lu...@ug...> - 2004-06-09 18:42:02
|
Hello- We are attempting to load some mass spec data into gus. Well, the version of gus that we have did not contain two of the relevant tables: DoTS.MassSpecFeature and DoTS.MassSpecSummary I created the MassSpecFeature view on DoTS.aafeatureimp and the table dots.massspecsummary. Now we need to generate the GUS objects for the tables for use in plug-ins. All of the oerl modules in GUS/Model/* are generated automagically. It looks like I could just copy some files and change the names. But they all say something like this: # THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE GUS::ObjRelP::Generator # PACKAGE. # # DO NOT EDIT!! # TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO InteractionType.pm.man # (or edit that file if it already exists) AND ADD THE FUNCTIONALITY THERE. # THEN RE-GENERATE THE GUS OBJECTS. Any word on how to use the Generator? Any help is appreciated. It might go well in the Wiki-wiki! Michael Luchtan |
|
From: Michael L. <lu...@ug...> - 2004-06-09 17:29:35
|
Sorry for the late reply... The multipartfilter has already been set-up. That was not the problem. You know, there are so many different logs to look at. It seems like lately I had been chasing my bugs down through the servlet.log file in the servlet directory. I looked at the catalina.out with notions of finding an error to send to the list, and found the java stack trace. Been busy tracking down bugs through catalina.out ever since. Thanks for the heads up on just having to restart tomcat after a change in the servletconfig file as opposed to having to recompile and all. Michael Luchtan On Mon, 2004-06-07 at 14:29, Angel Pizarro wrote: > Michael, this may be due to a change Steve made to using multi-part form > data. You need a jar file that handles this type of form and need to add > a section in your web.xml file. > > The jar file contains classes from com.oreilly.servlet: > cos-05Nov2002.jar > found here: > http://www.ibiblio.org/maven/servlets.com/jars/ > > The added section to web.xml is: > > <web-app> > ... > <filter> > <filter-name>multipartFilter</filter-name> > <filter-class>com.oreilly.servlet.MultipartFilter</filter-class> > <init-param> > <param-name>uploadDir</param-name> > <param-value>@TMP_DIR@</param-value> > </init-param> > </filter> > ... > </web-app> > > If this doesn't work, please email the list with the tomcat error log > output, of which I am sure there are many lines ;) > > > Angel > > Michael Luchtan wrote: > > >Hello- > >I am trying to get the "search genes by product field" working on our > >installation of the WDK. It's kind of hard to find the error. From the > >search page, I am taken to a page that says there are x number of > >entries, which correspond to the right answer, and says that it will > >display them, but there is nothing displayed in the table. > > > >I get the following message in the servlet.log: > >[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> GET request > >[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> No 'page' parameter in > >request, and no defaultPage set. > > > >Which is true. The url looks like: > >http://tcruzidb-gusdev.ctegd.uga.edu/tcruzidb-gusdev/servlet/servlet > > > >Where normally there is a ?page= after the servlet. Obviously the page > >is working, but I thought always there should be a ?page= when viewing a > >page via the servlet. Either way, how do I set my defaultPage if this > >is the problem? WHich of the conf files will do this? > >Also... I understand that (one of) the purposes(s) of the servlet.conf > >file is that you can make changes to it without having to recompile the > >java code and tomcat. This does not seem to work for me. If I make > >changes to the file in the servlet directory, nothing changes. Has > >anyone seen this error before? > > > >Michael Luchtan > > > > > > > > > >------------------------------------------------------- > >This SF.Net email is sponsored by: GNOME Foundation > >Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > >GNOME Users and Developers European Conference, 28-30th June in Norway > >http://2004/guadec.org > >_______________________________________________ > >Gusdev-gusdev mailing list > >Gus...@li... > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: GNOME Foundation > Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > GNOME Users and Developers European Conference, 28-30th June in Norway > http://2004/guadec.org > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Steve F. <st...@pc...> - 2004-06-09 15:20:14
|
paul- it looks like Dave did not commit his latest changes to cvs. he'll be in later tofday. sorry about that, steve Paul Mooney wrote: > Hi, > > I get an error when running the LoadGoOntology plugin. > It is up-to-date WRT cvs. > I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to > the one in my $GUS_HOME directory path. > Do I need a newer CBIL utilities ? > > Wed Jun 9 14:00:09 2004 loading all .ontology files in > /nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing > Wed Jun 9 14:00:10 2004 parsing all .ontology files in > preparation for inserting into database > Wed Jun 9 14:00:39 2004 parsing finished; loading ontology > into database > Can't locate object method "getDescription" via package > "CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load > "CBIL::Bio::GeneOntologyParser::Store"?) at > /nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm > line 452. > > Paul. > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: GNOME Foundation > Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > GNOME Users and Developers European Conference, 28-30th June in Norway > http://2004/guadec.org > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Paul M. <pj...@sa...> - 2004-06-09 13:42:23
|
Hi, I get an error when running the LoadGoOntology plugin. It is up-to-date WRT cvs. I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to the one in my $GUS_HOME directory path. Do I need a newer CBIL utilities ? Wed Jun 9 14:00:09 2004 loading all .ontology files in /nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing Wed Jun 9 14:00:10 2004 parsing all .ontology files in preparation for inserting into database Wed Jun 9 14:00:39 2004 parsing finished; loading ontology into database Can't locate object method "getDescription" via package "CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load "CBIL::Bio::GeneOntologyParser::Store"?) at /nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 452. Paul. |
|
From: jinal j. <jh...@us...> - 2004-06-08 04:32:13
|
I tried that and I get the same results as Michael |
|
From: MICHAEL L. <lu...@cs...> - 2004-06-07 22:40:06
|
Sucheta- I have tried the third query, Quick Search for dots genes, with the values 1 and DG.1 Both times I get the following: Official gene name/symbol from MGI or HUGO kit Gene description test gene Gene synonyms *** None *** Gene Model assigned to this gene Query failed, please try again later: java.sql.SQLException: ORA-00942: table or view does not exist DoTS Transcripts linked to this gene Query failed, please try again later: java.sql.SQLException: ORA-00936: missing expression Seems like it is working, except I assume the last parts you have not fixed or do not have the data in for yet. Michael Luchtan http://www.cs.uga.edu/~luchtan On Mon, 7 Jun 2004, Sucheta Tripathy wrote: > Yes, it is not a compilation issue, and should not be an issue with > environment variables either since I face problems at the web-browser level. > > I have freshly re-compiled the java sources and it works fine here, if some > one can just try from outside at > http://tyler-lab.bioinformatics.vt.edu/phytophthora/ > > and login to the site with login psojae and password Psojae and go to the > query.html page. > > Since the database is not having all the values, I have something for the > third query(at quick search for dots gene). It has a value 1. Here if I > provide 1, it queries the database properly, but if I do it from outside > the network, it does not move. > > Anyone had a similar problem? > > At 03:28 PM 6/7/2004 -0400, Angel Pizarro wrote: > >Sucheta Tripathy wrote: > > > >> > >>I am facing a strange problem every time I recompile. If I do the > >>re-compilation from office then querying from all computers in the > >>network works fine, but fails to work from outside and vice versa. > >OK, this is strange, but it is not a compiliation issue. A compilation > >issue would mean that you cannot compile the java files from > >cbil.gus.servlet package > > > >It also sounds liek you are installing to/from different places and/or > >using different environment variables depending on where you are > >installing the site from. In either case, this does not seem like an issue > >for the list in general. Please look at all of you environment and sources > >to make sure they are the same. If you are still having problems, the > >person that could help you the most is probably your systems > >administrator. As a last resort, please provide a more complete > >description of the problem, with examples if possible, and send it to the > >list again. Someone may have run into a similar situation, but we need > >more detail > > > >Angel > > > >>Any idea why this might be happening? > >> > >>If I will not need to restart tomcat or re-compile it will be great. > >> > >>Thanks > >> > >>Sucheta > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: GNOME Foundation > Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > GNOME Users and Developers European Conference, 28-30th June in Norway > http://2004/guadec.org > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Sucheta T. <su...@vb...> - 2004-06-07 20:08:36
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Yes, it is not a compilation issue, and should not be an issue with environment variables either since I face problems at the web-browser level. I have freshly re-compiled the java sources and it works fine here, if some one can just try from outside at http://tyler-lab.bioinformatics.vt.edu/phytophthora/ and login to the site with login psojae and password Psojae and go to the query.html page. Since the database is not having all the values, I have something for the third query(at quick search for dots gene). It has a value 1. Here if I provide 1, it queries the database properly, but if I do it from outside the network, it does not move. Anyone had a similar problem? At 03:28 PM 6/7/2004 -0400, Angel Pizarro wrote: >Sucheta Tripathy wrote: > >> >>I am facing a strange problem every time I recompile. If I do the >>re-compilation from office then querying from all computers in the >>network works fine, but fails to work from outside and vice versa. >OK, this is strange, but it is not a compiliation issue. A compilation >issue would mean that you cannot compile the java files from >cbil.gus.servlet package > >It also sounds liek you are installing to/from different places and/or >using different environment variables depending on where you are >installing the site from. In either case, this does not seem like an issue >for the list in general. Please look at all of you environment and sources >to make sure they are the same. If you are still having problems, the >person that could help you the most is probably your systems >administrator. As a last resort, please provide a more complete >description of the problem, with examples if possible, and send it to the >list again. Someone may have run into a similar situation, but we need >more detail > >Angel > >>Any idea why this might be happening? >> >>If I will not need to restart tomcat or re-compile it will be great. >> >>Thanks >> >>Sucheta > |
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From: Angel P. <an...@pc...> - 2004-06-07 19:27:41
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Sucheta Tripathy wrote: > > I am facing a strange problem every time I recompile. If I do the > re-compilation from office then querying from all computers in the > network works fine, but fails to work from outside and vice versa. > OK, this is strange, but it is not a compiliation issue. A compilation issue would mean that you cannot compile the java files from cbil.gus.servlet package It also sounds liek you are installing to/from different places and/or using different environment variables depending on where you are installing the site from. In either case, this does not seem like an issue for the list in general. Please look at all of you environment and sources to make sure they are the same. If you are still having problems, the person that could help you the most is probably your systems administrator. As a last resort, please provide a more complete description of the problem, with examples if possible, and send it to the list again. Someone may have run into a similar situation, but we need more detail Angel > Any idea why this might be happening? > > If I will not need to restart tomcat or re-compile it will be great. > > Thanks > > Sucheta |
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From: Sucheta T. <su...@vb...> - 2004-06-07 19:18:06
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I am facing a strange problem every time I recompile. If I do the re-compilation from office then querying from all computers in the network works fine, but fails to work from outside and vice versa. Any idea why this might be happening? If I will not need to restart tomcat or re-compile it will be great. Thanks Sucheta At 03:10 PM 6/7/2004 -0400, Angel Pizarro wrote: >John Iodice wrote: > >>The latter. >> >>But it's true that you don't have to recompile to get servlet-config >>updates. You must, however, reload the configuration by restarting the >>webapp or restarting Tomcat -- it persists from request to request. >> >>John >> >>On Mon, 2004-06-07 at 14:56, Sucheta Tripathy wrote: >> >> >>>Will this solve the re-compilation problem or the specific page problem? >>> >>> >It might solve both, actually. >I also got a blank page of results when using the newest wdk-classic until >I added the <filter> section to the web.xml file >I was not able to compile the new version of the wdk-classic until I >accounted for this jar. I accounted for ti by doing a cvs update to >InstallConfig.pm > >The installServlet.pl script should include this new jar in your classpath >as part of the install process, in addition to copying it to the >WEB-INF/lib directory. > >angel > >>>>Michael, this may be due to a change Steve made to using multi-part form >>>>data. You need a jar file that handles this type of form and need to add >>>>a section in your web.xml file. >>>> >>>>The jar file contains classes from com.oreilly.servlet: >>>>cos-05Nov2002.jar >>>>found here: >>>>http://www.ibiblio.org/maven/servlets.com/jars/ >>>> >>>>The added section to web.xml is: >>>> >>>><web-app> >>>>... >>>> <filter> >>>> <filter-name>multipartFilter</filter-name> >>>> <filter-class>com.oreilly.servlet.MultipartFilter</filter-class> >>>> <init-param> >>>> <param-name>uploadDir</param-name> >>>> <param-value>@TMP_DIR@</param-value> >>>> </init-param> >>>> </filter> >>>>... >>>></web-app> >>>> >>>>If this doesn't work, please email the list with the tomcat error log >>>>output, of which I am sure there are many lines ;) >>>> >>>> >>>>Angel >>>> >>>>Michael Luchtan wrote: >>>> >>>> >>>> >>>>>Hello- >>>>>I am trying to get the "search genes by product field" working on our >>>>>installation of the WDK. It's kind of hard to find the error. From the >>>>>search page, I am taken to a page that says there are x number of >>>>>entries, which correspond to the right answer, and says that it will >>>>>display them, but there is nothing displayed in the table. >>>>> >>>>>I get the following message in the servlet.log: >>>>>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> GET request >>>>>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> No 'page' parameter in >>>>>request, and no defaultPage set. >>>>> >>>>>Which is true. The url looks like: >>>>>http://tcruzidb-gusdev.ctegd.uga.edu/tcruzidb-gusdev/servlet/servlet >>>>> >>>>>Where normally there is a ?page= after the servlet. Obviously the page >>>>>is working, but I thought always there should be a ?page= when viewing a >>>>>page via the servlet. Either way, how do I set my defaultPage if this >>>>>is the problem? WHich of the conf files will do this? >>>>>Also... I understand that (one of) the purposes(s) of the servlet.conf >>>>>file is that you can make changes to it without having to recompile the >>>>>java code and tomcat. This does not seem to work for me. If I make >>>>>changes to the file in the servlet directory, nothing changes. Has >>>>>anyone seen this error before? >>>>> >>>>>Michael Luchtan >>>>> > > > >------------------------------------------------------- >This SF.Net email is sponsored by: GNOME Foundation >Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. >GNOME Users and Developers European Conference, 28-30th June in Norway >http://2004/guadec.org >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Angel P. <an...@pc...> - 2004-06-07 19:08:06
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John Iodice wrote: >The latter. > >But it's true that you don't have to recompile to get servlet-config >updates. You must, however, reload the configuration by restarting the >webapp or restarting Tomcat -- it persists from request to request. > >John > >On Mon, 2004-06-07 at 14:56, Sucheta Tripathy wrote: > > >>Will this solve the re-compilation problem or the specific page problem? >> >> >> It might solve both, actually. I also got a blank page of results when using the newest wdk-classic until I added the <filter> section to the web.xml file I was not able to compile the new version of the wdk-classic until I accounted for this jar. I accounted for ti by doing a cvs update to InstallConfig.pm The installServlet.pl script should include this new jar in your classpath as part of the install process, in addition to copying it to the WEB-INF/lib directory. angel >>>Michael, this may be due to a change Steve made to using multi-part form >>>data. You need a jar file that handles this type of form and need to add >>>a section in your web.xml file. >>> >>>The jar file contains classes from com.oreilly.servlet: >>>cos-05Nov2002.jar >>>found here: >>>http://www.ibiblio.org/maven/servlets.com/jars/ >>> >>>The added section to web.xml is: >>> >>><web-app> >>> ... >>> <filter> >>> <filter-name>multipartFilter</filter-name> >>> <filter-class>com.oreilly.servlet.MultipartFilter</filter-class> >>> <init-param> >>> <param-name>uploadDir</param-name> >>> <param-value>@TMP_DIR@</param-value> >>> </init-param> >>> </filter> >>>... >>></web-app> >>> >>>If this doesn't work, please email the list with the tomcat error log >>>output, of which I am sure there are many lines ;) >>> >>> >>>Angel >>> >>>Michael Luchtan wrote: >>> >>> >>> >>>>Hello- >>>>I am trying to get the "search genes by product field" working on our >>>>installation of the WDK. It's kind of hard to find the error. From the >>>>search page, I am taken to a page that says there are x number of >>>>entries, which correspond to the right answer, and says that it will >>>>display them, but there is nothing displayed in the table. >>>> >>>>I get the following message in the servlet.log: >>>>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> GET request >>>>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> No 'page' parameter in >>>>request, and no defaultPage set. >>>> >>>>Which is true. The url looks like: >>>>http://tcruzidb-gusdev.ctegd.uga.edu/tcruzidb-gusdev/servlet/servlet >>>> >>>>Where normally there is a ?page= after the servlet. Obviously the page >>>>is working, but I thought always there should be a ?page= when viewing a >>>>page via the servlet. Either way, how do I set my defaultPage if this >>>>is the problem? WHich of the conf files will do this? >>>>Also... I understand that (one of) the purposes(s) of the servlet.conf >>>>file is that you can make changes to it without having to recompile the >>>>java code and tomcat. This does not seem to work for me. If I make >>>>changes to the file in the servlet directory, nothing changes. Has >>>>anyone seen this error before? >>>> >>>>Michael Luchtan >>>> >>>> |
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From: John I. <io...@pc...> - 2004-06-07 19:00:59
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The latter. But it's true that you don't have to recompile to get servlet-config updates. You must, however, reload the configuration by restarting the webapp or restarting Tomcat -- it persists from request to request. John On Mon, 2004-06-07 at 14:56, Sucheta Tripathy wrote: > Will this solve the re-compilation problem or the specific page problem? > > > Michael, this may be due to a change Steve made to using multi-part form > > data. You need a jar file that handles this type of form and need to add > > a section in your web.xml file. > > > > The jar file contains classes from com.oreilly.servlet: > > cos-05Nov2002.jar > > found here: > > http://www.ibiblio.org/maven/servlets.com/jars/ > > > > The added section to web.xml is: > > > > <web-app> > > ... > > <filter> > > <filter-name>multipartFilter</filter-name> > > <filter-class>com.oreilly.servlet.MultipartFilter</filter-class> > > <init-param> > > <param-name>uploadDir</param-name> > > <param-value>@TMP_DIR@</param-value> > > </init-param> > > </filter> > > ... > > </web-app> > > > > If this doesn't work, please email the list with the tomcat error log > > output, of which I am sure there are many lines ;) > > > > > > Angel > > > > Michael Luchtan wrote: > > > >>Hello- > >>I am trying to get the "search genes by product field" working on our > >>installation of the WDK. It's kind of hard to find the error. From the > >>search page, I am taken to a page that says there are x number of > >>entries, which correspond to the right answer, and says that it will > >>display them, but there is nothing displayed in the table. > >> > >>I get the following message in the servlet.log: > >>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> GET request > >>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> No 'page' parameter in > >>request, and no defaultPage set. > >> > >>Which is true. The url looks like: > >>http://tcruzidb-gusdev.ctegd.uga.edu/tcruzidb-gusdev/servlet/servlet > >> > >>Where normally there is a ?page= after the servlet. Obviously the page > >>is working, but I thought always there should be a ?page= when viewing a > >>page via the servlet. Either way, how do I set my defaultPage if this > >>is the problem? WHich of the conf files will do this? > >>Also... I understand that (one of) the purposes(s) of the servlet.conf > >>file is that you can make changes to it without having to recompile the > >>java code and tomcat. This does not seem to work for me. If I make > >>changes to the file in the servlet directory, nothing changes. Has > >>anyone seen this error before? > >> > >>Michael Luchtan > >> > >> > >> > >> > >>------------------------------------------------------- > >>This SF.Net email is sponsored by: GNOME Foundation > >>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > >>GNOME Users and Developers European Conference, 28-30th June in Norway > >>http://2004/guadec.org > >>_______________________________________________ > >>Gusdev-gusdev mailing list > >>Gus...@li... > >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > >> > >> > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: GNOME Foundation > > Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > > GNOME Users and Developers European Conference, 28-30th June in Norway > > http://2004/guadec.org > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > |
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From: Sucheta T. <su...@vb...> - 2004-06-07 18:56:57
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Will this solve the re-compilation problem or the specific page problem? > Michael, this may be due to a change Steve made to using multi-part form > data. You need a jar file that handles this type of form and need to add > a section in your web.xml file. > > The jar file contains classes from com.oreilly.servlet: > cos-05Nov2002.jar > found here: > http://www.ibiblio.org/maven/servlets.com/jars/ > > The added section to web.xml is: > > <web-app> > ... > <filter> > <filter-name>multipartFilter</filter-name> > <filter-class>com.oreilly.servlet.MultipartFilter</filter-class> > <init-param> > <param-name>uploadDir</param-name> > <param-value>@TMP_DIR@</param-value> > </init-param> > </filter> > ... > </web-app> > > If this doesn't work, please email the list with the tomcat error log > output, of which I am sure there are many lines ;) > > > Angel > > Michael Luchtan wrote: > >>Hello- >>I am trying to get the "search genes by product field" working on our >>installation of the WDK. It's kind of hard to find the error. From the >>search page, I am taken to a page that says there are x number of >>entries, which correspond to the right answer, and says that it will >>display them, but there is nothing displayed in the table. >> >>I get the following message in the servlet.log: >>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> GET request >>[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> No 'page' parameter in >>request, and no defaultPage set. >> >>Which is true. The url looks like: >>http://tcruzidb-gusdev.ctegd.uga.edu/tcruzidb-gusdev/servlet/servlet >> >>Where normally there is a ?page= after the servlet. Obviously the page >>is working, but I thought always there should be a ?page= when viewing a >>page via the servlet. Either way, how do I set my defaultPage if this >>is the problem? WHich of the conf files will do this? >>Also... I understand that (one of) the purposes(s) of the servlet.conf >>file is that you can make changes to it without having to recompile the >>java code and tomcat. This does not seem to work for me. If I make >>changes to the file in the servlet directory, nothing changes. Has >>anyone seen this error before? >> >>Michael Luchtan >> >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by: GNOME Foundation >>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. >>GNOME Users and Developers European Conference, 28-30th June in Norway >>http://2004/guadec.org >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: GNOME Foundation > Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. > GNOME Users and Developers European Conference, 28-30th June in Norway > http://2004/guadec.org > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
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From: Angel P. <an...@pc...> - 2004-06-07 18:27:26
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Michael, this may be due to a change Steve made to using multi-part form data. You need a jar file that handles this type of form and need to add a section in your web.xml file. The jar file contains classes from com.oreilly.servlet: cos-05Nov2002.jar found here: http://www.ibiblio.org/maven/servlets.com/jars/ The added section to web.xml is: <web-app> ... <filter> <filter-name>multipartFilter</filter-name> <filter-class>com.oreilly.servlet.MultipartFilter</filter-class> <init-param> <param-name>uploadDir</param-name> <param-value>@TMP_DIR@</param-value> </init-param> </filter> ... </web-app> If this doesn't work, please email the list with the tomcat error log output, of which I am sure there are many lines ;) Angel Michael Luchtan wrote: >Hello- >I am trying to get the "search genes by product field" working on our >installation of the WDK. It's kind of hard to find the error. From the >search page, I am taken to a page that says there are x number of >entries, which correspond to the right answer, and says that it will >display them, but there is nothing displayed in the table. > >I get the following message in the servlet.log: >[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> GET request >[Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> No 'page' parameter in >request, and no defaultPage set. > >Which is true. The url looks like: >http://tcruzidb-gusdev.ctegd.uga.edu/tcruzidb-gusdev/servlet/servlet > >Where normally there is a ?page= after the servlet. Obviously the page >is working, but I thought always there should be a ?page= when viewing a >page via the servlet. Either way, how do I set my defaultPage if this >is the problem? WHich of the conf files will do this? >Also... I understand that (one of) the purposes(s) of the servlet.conf >file is that you can make changes to it without having to recompile the >java code and tomcat. This does not seem to work for me. If I make >changes to the file in the servlet directory, nothing changes. Has >anyone seen this error before? > >Michael Luchtan > > > > >------------------------------------------------------- >This SF.Net email is sponsored by: GNOME Foundation >Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. >GNOME Users and Developers European Conference, 28-30th June in Norway >http://2004/guadec.org >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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From: Michael L. <lu...@ug...> - 2004-06-07 17:56:59
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Hello- I am trying to get the "search genes by product field" working on our installation of the WDK. It's kind of hard to find the error. From the search page, I am taken to a page that says there are x number of entries, which correspond to the right answer, and says that it will display them, but there is nothing displayed in the table. I get the following message in the servlet.log: [Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> GET request [Jun 7, 2004 1:41:44 PM] <SiteServlet:MSG> No 'page' parameter in request, and no defaultPage set. Which is true. The url looks like: http://tcruzidb-gusdev.ctegd.uga.edu/tcruzidb-gusdev/servlet/servlet Where normally there is a ?page= after the servlet. Obviously the page is working, but I thought always there should be a ?page= when viewing a page via the servlet. Either way, how do I set my defaultPage if this is the problem? WHich of the conf files will do this? Also... I understand that (one of) the purposes(s) of the servlet.conf file is that you can make changes to it without having to recompile the java code and tomcat. This does not seem to work for me. If I make changes to the file in the servlet directory, nothing changes. Has anyone seen this error before? Michael Luchtan |
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From: Bindu G. <bi...@pc...> - 2004-06-05 13:48:40
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yes, there is: DoTS.ScaffoldGapFeature in combination with DoTS.NALocation. Bindu On Jun 4, 2004, at 3:37 PM, Sucheta Tripathy wrote: > Hello all, > > I was wondering if there is a place to store the gap information in a > scaffold in GUS? > > Thanks > > Sucheta > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the new InstallShield X. >> From Windows to Linux, servers to mobile, InstallShield X is the one > installation-authoring solution that does it all. Learn more and > evaluate today! http://www.installshield.com/Dev2Dev/0504 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Sucheta T. <su...@vb...> - 2004-06-04 19:37:24
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Hello all, I was wondering if there is a place to store the gap information in a scaffold in GUS? Thanks Sucheta |
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From: Steve F. <st...@pc...> - 2004-06-04 14:27:58
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why do we have db_name and db_identifier in NALocation? steve |
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From: Steve F. <st...@pc...> - 2004-06-04 14:26:48
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folks- Following our new documentation paradigm, rather than answering by email, I have answered Josef's question about subclass_view by writing a page on the GUS Wiki about Subclassing in GUS. steve |
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