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Re: [Gusdev-gusdev] "RE-GENERATE THE GUS OBJECTS"
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From: Michael L. <lu...@ug...> - 2004-06-09 20:46:09
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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
> >
> >
>
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