Re: [Gusdev-gusdev] "RE-GENERATE THE GUS OBJECTS"

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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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>-------------------------------------------------------
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>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
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>>>