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Re: [Gusdev-gusdev] "RE-GENERATE THE GUS OBJECTS"
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From: Steve F. <sfi...@pc...> - 2004-06-11 15:20:23
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michael- oops, i had forgotten to check in my change to Oracle.pm. done.
about the sequences, sorry about that. yeah, it looks like you have to
fix the sequence. I don't know how to do that.
steve
Michael Luchtan wrote:
>Steve-
>The problem was not quite fixed. SInce this is all new, the first thing
>I have to do is ga +meta , right? Well, first there was a compilation
>problem, which was easily fixed. I don't have cvs write, so you might
>want to have someone else do it.
>GUS::ObjRelP::DbiTable.pm wants to call a method nextValSelect on the
>Oracle or Postgres object. There is such a function in PostgreSQL,
>called nextValSelect, but commented with the name nextValSQL. Anyway, I
>changed the nextValSQL in Oracle.pm to nextValSelect and all worked
>fine. Seems like that is the correct thing to do. Unfortunately, our
>Sequences have somehow been screwed up. From the sqlplus prompt:
>
>SQL> select core.algorithminvocation_sq.nextval from dual;
>
> NEXTVAL
>----------
> 62
>
>SQL> select core.algorithmimplementation_sq.nextval from dual;
>
> NEXTVAL
>----------
> 62
>SQL> select MAX(algorithm_invocation_id) from core.algorithminvocation;
>
>MAX(ALGORITHM_INVOCATION_ID)
>----------------------------
> 30288
>
>
>And thus the ga +meta has a pk constraint error. Here is the output:
>gus_home]# ga +meta
> <Core::Algorithm>
> <algorithm_id>2</algorithm_id>
> <name>GA-Plugin</name>
> <description>GUS application framework for plugins</description>
> <modification_date>29-OCT-03</modification_date>
> <Core::AlgorithmImplementation>
> <cvs_revision>1.49</cvs_revision>
> <cvs_tag> </cvs_tag>
> <executable>GUS::PluginMgr::GusApplication</executable>
> <executable_md5>e291775acbf95c5ed6bae9024ad78e79</executable_md5>
> <description>update for GUS 3.0</description>
> <Core::AlgorithmInvocation>
> <start_time>SYSDATE</start_time>
> <end_time>SYSDATE</end_time>
> <machine_id>0</machine_id>
> <cpus_used>1</cpus_used>
> <result>meta</result>
> </Core::AlgorithmInvocation>
> </Core::AlgorithmImplementation>
> <user_read>1</user_read>
> <user_write>1</user_write>
> <group_read>1</group_read>
> <group_write>1</group_write>
> <other_read>1</other_read>
> <other_write>0</other_write>
> <row_user_id>3</row_user_id>
> <row_group_id>2</row_group_id>
> <row_project_id>2</row_project_id>
> <row_alg_invocation_id>1</row_alg_invocation_id>
> </Core::Algorithm>
>DBD::Oracle::st execute failed: ORA-00001: unique constraint
>(CORE.PK_ALGORITHMINVOCATION) violated (DB\
>D 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, algorithm_i\
>mplementation_id, row_project_id, algorithm_invocation_id, 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, 63, 2, 63, 1, 2, meta, 1, 1, 1, 1, 0, 0 at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/D\
>biDbHandle.pm line 185
>
>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x861c7a0)', '^J SQL ERROR!! i\
>nvolving^J ^J INSERT INTO Core.AlgorithmInvocati...') called at
>/var/local/gus_home/lib/perl/GUS/Obj\
>RelP/DbiDbHandle.pm line 148
>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x861c7a0)', 'GUS::ObjRelP::\
>DbiDbHandle::st=HASH(0x8740df4)', 'ARRAY(0x8740e84)', '^J INSERT INTO
>Core.AlgorithmInvocation ( en\
>d_time, row_user_...') called at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>
>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ac4d0)',\
> 'HASH(0x8746bf0)') called at
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>
>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ac4d0)') called at\
> /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>
>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ac4d0)', undef, 1) c\
>alled at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>
>GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmImplementation=HASH(0x869\
>6a18)', 'GUS::Model::Core::AlgorithmInvocation') called at
>/var/local/gus_home/lib/perl/GUS/Model/GusRo\
>w.pm line 1745
>
>GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplementation=HASH(0x8696a18\
>)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x8696a18)', undef, \
>1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>
>GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x861c710)', 'GUS::\
>Model::Core::AlgorithmImplementation') called at
>/var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line \
>1745
>
>GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x861c710)') called at \
>/var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
>GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x861c710)') called at /var/local/\
>gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 355
>
>GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c\
>)', undef) called at
>/var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', u\
>ndef) 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
>
>
>
>We will write a script to reset all our sequences by selecting the max.
>Don't know how this event transpired though...
>
>Michael Luchtan
>
>
>
>
>On Thu, 2004-06-10 at 17:36, Steve Fischer wrote:
>
>
>>Michael-
>>
>>i think i have fixed the ga problem.
>>
>>do this:
>> - get the latest from cvs.
>> - rm $GUS_HOME/lib/perl/GUS/ObjRelP/*.pm
>> - rm $GUS_HOME/lib/perl/GUS/Model/GusRow.pm
>> - build GUS install -append
>>
>>steve
>>
>>Michael Luchtan wrote:
>>
>>
>>>Dave-
>>>That seemed to do it. I had to create the core.workflonode view, and
>>>core.workflownodeimp, then insert them into tableinfo.
>>>So I have successfully done a
>>>build GUS install -append
>>>without any crashes.
>>>Still can't run the ga though. Steve said he was working on it. I
>>>don't think that there is anything that happens with the following
>>>command that alters the database, so I don't see how it would have reset
>>>the SEQ.
>>>
>>>Thanks,
>>>Michael Luchtan
>>>
>>>
>>>
>>>On Thu, 2004-06-10 at 15:22, Dave Barkan wrote:
>>>
>>>
>>>
>>>>I may have seen something similar to this a few months ago. Make sure
>>>>that the table "Core.WorkflowNode" is in your schema and in your
>>>>TableInfo (and Core.WorkflowNodeImp for that matter).
>>>>
>>>>Dave
>>>>
>>>>On Thu, 10 Jun 2004, Michael Luchtan wrote:
>>>>
>>>>
>>>>
>>>>
>>>>>Steve-
>>>>>Not all of them, just three:
>>>>>[root@mkiwi install]# cd ../GUS/Model/src/java/org/gusdb/model/Core/
>>>>>[root@mkiwi Core]# ls WorkflowN*
>>>>>WorkflowNoOpNode.java WorkflowNoOpNode_Row.java
>>>>>WorkflowNoOpNode_Table.java
>>>>>
>>>>>Why is this? I guess that is why it is complaining about not finding
>>>>>the workflownode object. But these objects should be dynamically
>>>>>created, no? Am I missing something in my core.tableinfo or something?
>>>>>
>>>>>Thanks for the quick reply. I appreciate it.
>>>>>Michael Luchtan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>On Thu, 2004-06-10 at 15:09, Steve Fischer wrote:
>>>>>
>>>>>
>>>>>
>>>>>>about WorkflowNode: is the file in the following dir?
>>>>>>
>>>>>>[sfischer@pythia Core]$cd
>>>>>>$PROJECT_HOME/GUS/Model/src/java/org/gusdb/model/Core/
>>>>>>[sfischer@pythia Core]$ ls WorkflowN*
>>>>>>WorkflowNode.java WorkflowNode_Table.java WorkflowNoOpNode_Row.java
>>>>>>WorkflowNode_Row.java WorkflowNoOpNode.java WorkflowNoOpNode_Table.java
>>>>>>
>>>>>>about ga, i have reproduced the problem here, and will let you know as
>>>>>>soon as i have fixed it. it is probably a result of the new postgres
>>>>>>compatibility code.
>>>>>>
>>>>>>steve
>>>>>>
>>>>>>Michael Luchtan wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>So here is the current situation. I have the newest GUS, install, and
>>>>>>>CBIL available. When I attempt to build GUS by executing the following
>>>>>>>command:
>>>>>>>build GUS install -append
>>>>>>>Everything seems to go fine until we get the following error message:
>>>>>>> [exec] generating java object for DoTS::TranslatedAASequence
>>>>>>> [exec] generating java object for RAD3::SpotFamily
>>>>>>> [mkdir] Created dir:
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/hand_edited/App
>>>>>>> [copy] Copying 2 files to
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS
>>>>>>> [copy] Copying 1 file to
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SRes
>>>>>>> [echo] Starting target: JavaModel
>>>>>>> [echo] .
>>>>>>> [echo] Installing GUS/Model
>>>>>>> [copy] Copying 1291 files to /var/local/gus_home/lib/perl/GUS/Model
>>>>>>> [mkdir] Created dir: /var/local/checkout/GUS/Model/classes
>>>>>>> [javac] Compiling 1086 source files to
>>>>>>>/var/local/checkout/GUS/Model/classes
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:119: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>setToWorkflowNode(org.gusdb.model.Core.WorkflowNode
>>>>>>>to_workflow_node_id){
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:123: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public org.gusdb.model.Core.WorkflowNode
>>>>>>>getToWorkflowNode(boolean retrieveFromDb)
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:129: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>setFromWorkflowNode(org.gusdb.model.Core.WorkflowNode
>>>>>>>from_workflow_node_id){
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:133: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public org.gusdb.model.Core.WorkflowNode
>>>>>>>getFromWorkflowNode(boolean retrieveFromDb)
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/Workflow_Row.java:175: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/GroupInfo_Row.java:3136: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:2740: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:2306: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>addWorkflowNode_IAmA_algorithminvocation(org.gusdb.model.Core.WorkflowNode workflownode_iama_algorithminvocation){
>>>>>>>
>>>>>>>[javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:2702: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>addWorkflowNode_IAmA_rowalginvocation(org.gusdb.model.Core.WorkflowNode
>>>>>>>workflownode_iama_rowalginvocation){
>>>>>>>
>>>>>>>[javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/UserInfo_Row.java:1847: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] public void
>>>>>>>addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:126: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] return
>>>>>>>(org.gusdb.model.Core.WorkflowNode)getParent("to_workflow_node_id",
>>>>>>>retrieveFromDb);
>>>>>>> [javac] ^
>>>>>>> [javac]
>>>>>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:136: cannot resolve symbol
>>>>>>> [javac] symbol : class WorkflowNode
>>>>>>> [javac] location: package Core
>>>>>>> [javac] return
>>>>>>>(org.gusdb.model.Core.WorkflowNode)getParent("from_workflow_node_id",
>>>>>>>retrieveFromDb);
>>>>>>> [javac] ^
>>>>>>> [javac] 12 errors
>>>>>>>
>>>>>>>BUILD FAILED
>>>>>>>file:/var/local/checkout/install/build.xml:235: Compile failed; see the
>>>>>>>compiler error output for details.
>>>>>>>
>>>>>>>Total time: 14 minutes 11 seconds
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>Who knows why this isn't working, but I think I know why ga and such is
>>>>>>>no longer working. When I attempt to run anything with ga, I get PK
>>>>>>>violations. I am under the impressions that ga (or perhaps somewhere
>>>>>>>else) has an internal counter to deal with things like primary keys like
>>>>>>>algorithm_implementation_id or algorithm_invocation_id when inserting
>>>>>>>new entries.
>>>>>>>Here is the error I get when trying to update ga for the new SubmitRow
>>>>>>>plugin:
>>>>>>>
>>>>>>>[root@mkiwi install]# ga +update GUS::Common::Plugin::SubmitRow
>>>>>>>DBD::Oracle::st execute failed: ORA-00001: unique constraint
>>>>>>>(CORE.PK_ALGORITHMIMPLEMENTATION) violated (DBD ERROR: OCIStmtExecute)
>>>>>>>at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
>>>>>>>
>>>>>>>SQL ERROR!! involving
>>>>>>>
>>>>>>> INSERT INTO Core.AlgorithmImplementation ( description,
>>>>>>>row_user_id, user_write, group_write, executable_md5,
>>>>>>>algorithm_implementation_id, row_project_id, cvs_revision, group_read,
>>>>>>>row_group_id, cvs_tag, executable, other_read, modification_date,
>>>>>>>user_read, algorithm_id, row_alg_invocation_id, other_write )
>>>>>>> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?,
>>>>>>>? )
>>>>>>>Values: make consistent with GUS 3.0, 4, 1, 1,
>>>>>>>2e3da77408e21e4e9d7b57ec9b8d412d, 24, 2, 1.8, 1, 2, ,
>>>>>>>GUS::Common::Plugin::SubmitRow, 1, 1, 3, 1, 0 at
>>>>>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>>>>>>>
>>>>>>>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85f2b00)', '^J SQL ERROR!! involving^J ^J INSERT INTO Core.AlgorithmImplemen...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>>>>>>>
>>>>>>>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85f2b00)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8773514)', 'ARRAY(0x877355c)', '^J INSERT INTO Core.AlgorithmImplementation ( description, ro...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>>>>>>>
>>>>>>>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmImplementation=HASH(0x8713d68)', 'HASH(0x81ef630)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>>>>>>>
>>>>>>>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmImplementation=HASH(0x8713d68)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>>>>>>>
>>>>>>>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x8713d68)', undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>>>>>>>
>>>>>>>GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x86f83e8)', 'GUS::Model::Core::AlgorithmImplementation') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
>>>>>>>
>>>>>>>GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x86f83e8)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>>>>>>>
>>>>>>>GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x86f83e8)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 812
>>>>>>>
>>>>>>>GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 1, 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 466
>>>>>>>
>>>>>>>GUS::PluginMgr::GusApplication::doMajorMode_Update('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
>>>>>>>[root@mkiwi install]#
>>>>>>>
>>>>>>>
>>>>>>>How can I get these counters reset? Or is this the wrong direction for
>>>>>>>finding a solution to the problem?
>>>>>>>
>>>>>>>Thanks,
>>>>>>>Michael Luchtan
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>On Wed, 2004-06-09 at 17:00, Steve Fischer wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>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
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>>>>>>>>>>>>>_______________________________________________
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>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>-------------------------------------------------------
>>>>>>>>>>>>This SF.Net email is sponsored by: GNOME Foundation
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>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>-------------------------------------------------------
>>>>>>>>>>>This SF.Net email is sponsored by: GNOME Foundation
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>>>>>>>>>>>_______________________________________________
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>
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